From 133fd3adfc76216d8808ed7200e7278bdaf87488 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sat, 12 Nov 2016 11:05:51 +0100
Subject: [PATCH 1/2] Quote all paths in converter tools

---
 lib/galaxy/datatypes/converters/bed_to_fli_converter.xml    | 2 +-
 lib/galaxy/datatypes/converters/bed_to_gff_converter.xml    | 2 +-
 lib/galaxy/datatypes/converters/bed_to_tabix_converter.xml  | 2 +-
 .../converters/bedgraph_to_array_tree_converter.xml         | 2 +-
 .../datatypes/converters/bedgraph_to_bigwig_converter.xml   | 2 +-
 lib/galaxy/datatypes/converters/cml_to_inchi_converter.xml  | 2 +-
 lib/galaxy/datatypes/converters/cml_to_mol2_converter.xml   | 2 +-
 lib/galaxy/datatypes/converters/cml_to_sdf_converter.xml    | 2 +-
 lib/galaxy/datatypes/converters/cml_to_smi_converter.xml    | 4 ++--
 .../datatypes/converters/encodepeak_to_bgzip_converter.xml  | 2 +-
 .../datatypes/converters/encodepeak_to_tabix_converter.xml  | 2 +-
 lib/galaxy/datatypes/converters/fasta_to_2bit.xml           | 2 +-
 .../converters/fasta_to_bowtie_base_index_converter.xml     | 4 ++--
 .../converters/fasta_to_bowtie_color_index_converter.xml    | 4 ++--
 lib/galaxy/datatypes/converters/fasta_to_len.xml            | 2 +-
 .../datatypes/converters/fasta_to_tabular_converter.xml     | 2 +-
 lib/galaxy/datatypes/converters/fastq_to_fqtoc.xml          | 2 +-
 .../datatypes/converters/fastqsolexa_to_fasta_converter.xml | 2 +-
 .../datatypes/converters/fastqsolexa_to_qual_converter.xml  | 2 +-
 lib/galaxy/datatypes/converters/gff_to_bed_converter.xml    | 2 +-
 lib/galaxy/datatypes/converters/gff_to_bgzip_converter.xml  | 2 +-
 lib/galaxy/datatypes/converters/gff_to_fli_converter.xml    | 2 +-
 .../converters/gff_to_interval_index_converter.xml          | 2 +-
 lib/galaxy/datatypes/converters/gff_to_tabix_converter.xml  | 2 +-
 lib/galaxy/datatypes/converters/inchi_to_cml_converter.xml  | 2 +-
 lib/galaxy/datatypes/converters/inchi_to_mol2_converter.xml | 2 +-
 lib/galaxy/datatypes/converters/inchi_to_mol_converter.xml  | 2 +-
 lib/galaxy/datatypes/converters/inchi_to_sdf_converter.xml  | 2 +-
 lib/galaxy/datatypes/converters/inchi_to_smi_converter.xml  | 2 +-
 .../datatypes/converters/interval_to_bed12_converter.xml    | 2 +-
 .../datatypes/converters/interval_to_bed6_converter.xml     | 2 +-
 .../datatypes/converters/interval_to_bed_converter.xml      | 2 +-
 .../converters/interval_to_bedstrict_converter.xml          | 2 +-
 .../datatypes/converters/interval_to_bgzip_converter.xml    | 2 +-
 .../datatypes/converters/interval_to_bigwig_converter.xml   | 6 +++---
 lib/galaxy/datatypes/converters/interval_to_coverage.xml    | 2 +-
 .../converters/interval_to_interval_index_converter.xml     | 2 +-
 .../datatypes/converters/interval_to_tabix_converter.xml    | 2 +-
 lib/galaxy/datatypes/converters/len_to_linecount.xml        | 2 +-
 lib/galaxy/datatypes/converters/maf_to_fasta_converter.xml  | 2 +-
 .../datatypes/converters/maf_to_interval_converter.xml      | 2 +-
 lib/galaxy/datatypes/converters/mol2_to_cml_converter.xml   | 2 +-
 lib/galaxy/datatypes/converters/mol2_to_inchi_converter.xml | 2 +-
 lib/galaxy/datatypes/converters/mol2_to_mol_converter.xml   | 2 +-
 lib/galaxy/datatypes/converters/mol2_to_sdf_converter.xml   | 2 +-
 lib/galaxy/datatypes/converters/mol2_to_smi_converter.xml   | 2 +-
 lib/galaxy/datatypes/converters/mol_to_cml_converter.xml    | 2 +-
 lib/galaxy/datatypes/converters/mol_to_inchi_converter.xml  | 2 +-
 lib/galaxy/datatypes/converters/mol_to_mol2_converter.xml   | 2 +-
 .../converters/picard_interval_list_to_bed6_converter.xml   | 2 +-
 .../converters/pileup_to_interval_index_converter.xml       | 2 +-
 .../datatypes/converters/ref_to_seq_taxonomy_converter.xml  | 2 +-
 lib/galaxy/datatypes/converters/sam_to_bam.xml              | 2 +-
 lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml | 6 +++---
 lib/galaxy/datatypes/converters/sdf_to_cml_converter.xml    | 2 +-
 lib/galaxy/datatypes/converters/sdf_to_inchi_converter.xml  | 2 +-
 lib/galaxy/datatypes/converters/sdf_to_mol2_converter.xml   | 2 +-
 lib/galaxy/datatypes/converters/sdf_to_smi_converter.xml    | 4 ++--
 lib/galaxy/datatypes/converters/smi_to_cml_converter.xml    | 2 +-
 lib/galaxy/datatypes/converters/smi_to_inchi_converter.xml  | 2 +-
 lib/galaxy/datatypes/converters/smi_to_mol2_converter.xml   | 2 +-
 lib/galaxy/datatypes/converters/smi_to_mol_converter.xml    | 2 +-
 lib/galaxy/datatypes/converters/smi_to_sdf_converter.xml    | 2 +-
 lib/galaxy/datatypes/converters/smi_to_smi_converter.xml    | 4 ++--
 lib/galaxy/datatypes/converters/tabular_to_dbnsfp.xml       | 2 +-
 lib/galaxy/datatypes/converters/vcf_to_bgzip_converter.xml  | 2 +-
 .../converters/vcf_to_interval_index_converter.xml          | 2 +-
 lib/galaxy/datatypes/converters/vcf_to_tabix_converter.xml  | 2 +-
 lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml | 2 +-
 .../datatypes/converters/wiggle_to_array_tree_converter.xml | 2 +-
 .../datatypes/converters/wiggle_to_simple_converter.xml     | 4 ++--
 lib/galaxy/tools/imp_exp/exp_history_to_archive.xml         | 2 +-
 72 files changed, 82 insertions(+), 82 deletions(-)

diff --git a/lib/galaxy/datatypes/converters/bed_to_fli_converter.xml b/lib/galaxy/datatypes/converters/bed_to_fli_converter.xml
index d1caf69b95c..3bda5c9d4df 100644
--- a/lib/galaxy/datatypes/converters/bed_to_fli_converter.xml
+++ b/lib/galaxy/datatypes/converters/bed_to_fli_converter.xml
@@ -1,7 +1,7 @@
 <tool id="CONVERTER_bed_to_fli_0" name="Convert BED to Feature Location Index">
   <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
   <!-- Used on the metadata edit page. -->
-  <command interpreter="python">interval_to_fli.py -F bed $input1 $output1</command>
+  <command interpreter="python">interval_to_fli.py -F bed '$input1' '$output1'</command>
   <inputs>
     <param format="bed" name="input1" type="data" label="Choose BED file"/>
   </inputs>
diff --git a/lib/galaxy/datatypes/converters/bed_to_gff_converter.xml b/lib/galaxy/datatypes/converters/bed_to_gff_converter.xml
index 548acbd8ec9..1c4151fb61f 100644
--- a/lib/galaxy/datatypes/converters/bed_to_gff_converter.xml
+++ b/lib/galaxy/datatypes/converters/bed_to_gff_converter.xml
@@ -1,7 +1,7 @@
 <tool id="CONVERTER_bed_to_gff_0" name="Convert BED to GFF" version="2.0.0">
   <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
   <!-- Used on the metadata edit page. -->
-  <command interpreter="python">bed_to_gff_converter.py $input1 $output1</command>
+  <command interpreter="python">bed_to_gff_converter.py '$input1' '$output1'</command>
   <inputs>
     <param format="bed" name="input1" type="data" label="Choose BED file"/>
   </inputs>
diff --git a/lib/galaxy/datatypes/converters/bed_to_tabix_converter.xml b/lib/galaxy/datatypes/converters/bed_to_tabix_converter.xml
index b511c6ac26f..22729583613 100644
--- a/lib/galaxy/datatypes/converters/bed_to_tabix_converter.xml
+++ b/lib/galaxy/datatypes/converters/bed_to_tabix_converter.xml
@@ -1,6 +1,6 @@
 <tool id="CONVERTER_bed_to_tabix_0" name="Convert BED to tabix" version="1.0.0" hidden="true">
 <!--  <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
-  <command interpreter="python">interval_to_tabix_converter.py -P bed $input1 $bgzip $output1</command>
+  <command interpreter="python">interval_to_tabix_converter.py -P bed '$input1' '$bgzip' '$output1'</command>
   <inputs>
     <page>
         <param format="bed" name="input1" type="data" label="Choose BED file"/>
diff --git a/lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.xml b/lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.xml
index a7538b6142b..d1baafbe038 100644
--- a/lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.xml
+++ b/lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.xml
@@ -1,6 +1,6 @@
 <tool id="CONVERTER_BedGraph_0" name="Index BedGraph for Track Viewer" hidden="true">
   <!-- Used internally to generate track indexes -->
-  <command interpreter="python">bedgraph_to_array_tree_converter.py $input $output</command>
+  <command interpreter="python">bedgraph_to_array_tree_converter.py '$input' '$output'</command>
   <inputs>
     <page>
       <param format="bedgraph" name="input" type="data" label="Choose BedGraph"/>
diff --git a/lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml b/lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml
index d4cd7d01a36..f91925dfe12 100644
--- a/lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml
+++ b/lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml
@@ -3,7 +3,7 @@
   <requirements>
       <requirement type="package">ucsc_tools</requirement>
   </requirements>
-  <command>grep -v "^track" $input | wigToBigWig -clip stdin $chromInfo $output</command>
+  <command>grep -v "^track" '$input' | wigToBigWig -clip stdin $chromInfo '$output'</command>
   <inputs>
       <param format="bedgraph" name="input" type="data" label="Choose wiggle"/>
    </inputs>
diff --git a/lib/galaxy/datatypes/converters/cml_to_inchi_converter.xml b/lib/galaxy/datatypes/converters/cml_to_inchi_converter.xml
index f6bc53f7f0d..36e3deca3ae 100644
--- a/lib/galaxy/datatypes/converters/cml_to_inchi_converter.xml
+++ b/lib/galaxy/datatypes/converters/cml_to_inchi_converter.xml
@@ -6,7 +6,7 @@
     </requirements>
     <command>
 <![CDATA[
-        obabel -icml "${input}" -oinchi -O "${output}" -e 2>&1
+        obabel -icml '${input}' -oinchi -O '${output}' -e 2>&1
 ]]>
     </command>
     <inputs>
diff --git a/lib/galaxy/datatypes/converters/cml_to_mol2_converter.xml b/lib/galaxy/datatypes/converters/cml_to_mol2_converter.xml
index cf07535ed8e..5f279f8d3e9 100644
--- a/lib/galaxy/datatypes/converters/cml_to_mol2_converter.xml
+++ b/lib/galaxy/datatypes/converters/cml_to_mol2_converter.xml
@@ -6,7 +6,7 @@
     </requirements>
     <command>
 <![CDATA[
-        obabel -icml "${input}" -omol2 -O "${output}" -e 2>&1
+        obabel -icml '${input}' -omol2 -O '${output}' -e 2>&1
 ]]>
     </command>
     <inputs>
diff --git a/lib/galaxy/datatypes/converters/cml_to_sdf_converter.xml b/lib/galaxy/datatypes/converters/cml_to_sdf_converter.xml
index f5e238251b6..5aaee721ea3 100644
--- a/lib/galaxy/datatypes/converters/cml_to_sdf_converter.xml
+++ b/lib/galaxy/datatypes/converters/cml_to_sdf_converter.xml
@@ -6,7 +6,7 @@
     </requirements>
     <command>
 <![CDATA[
-        obabel -icml "${input}" -osdf "${output}" -e 2>&1
+        obabel -icml '${input}' -osdf '${output}' -e 2>&1
 ]]>
     </command>
     <inputs>
diff --git a/lib/galaxy/datatypes/converters/cml_to_smi_converter.xml b/lib/galaxy/datatypes/converters/cml_to_smi_converter.xml
index 7fae58c4551..d4f3554398a 100644
--- a/lib/galaxy/datatypes/converters/cml_to_smi_converter.xml
+++ b/lib/galaxy/datatypes/converters/cml_to_smi_converter.xml
@@ -7,13 +7,13 @@
     <command >
 <![CDATA[
         obabel
-            -icml "${input}"
+            -icml '${input}'
             #if $can:
                 -ocan
             #else:
                 -osmi
             #end if
-            -O "${output}"
+            -O '${output}'
             -e
             $remove_h
             #if $iso_chi or $can or $exp_h:
diff --git a/lib/galaxy/datatypes/converters/encodepeak_to_bgzip_converter.xml b/lib/galaxy/datatypes/converters/encodepeak_to_bgzip_converter.xml
index 0779e6e7574..194d5a452bc 100644
--- a/lib/galaxy/datatypes/converters/encodepeak_to_bgzip_converter.xml
+++ b/lib/galaxy/datatypes/converters/encodepeak_to_bgzip_converter.xml
@@ -4,7 +4,7 @@
                                   -c ${input1.metadata.chromCol} 
                                   -s ${input1.metadata.startCol} 
                                   -e ${input1.metadata.endCol} 
-                                  $input1 $output1
+                                  '$input1' '$output1'
   </command>
   <inputs>
     <page>
diff --git a/lib/galaxy/datatypes/converters/encodepeak_to_tabix_converter.xml b/lib/galaxy/datatypes/converters/encodepeak_to_tabix_converter.xml
index 470dfb9936e..0524bfdac78 100644
--- a/lib/galaxy/datatypes/converters/encodepeak_to_tabix_converter.xml
+++ b/lib/galaxy/datatypes/converters/encodepeak_to_tabix_converter.xml
@@ -4,7 +4,7 @@
                                   -c ${input1.metadata.chromCol} 
                                   -s ${input1.metadata.startCol} 
                                   -e ${input1.metadata.endCol} 
-                                  $input1 $bgzip $output1    
+                                  '$input1' '$bgzip' '$output1'
   </command>
   <inputs>
     <page>
diff --git a/lib/galaxy/datatypes/converters/fasta_to_2bit.xml b/lib/galaxy/datatypes/converters/fasta_to_2bit.xml
index b4bd82c03a4..a8e3bb3204f 100644
--- a/lib/galaxy/datatypes/converters/fasta_to_2bit.xml
+++ b/lib/galaxy/datatypes/converters/fasta_to_2bit.xml
@@ -4,7 +4,7 @@
     <requirements>
         <requirement type="package">ucsc_tools</requirement>
     </requirements>
-    <command>faToTwoBit $input $output</command>
+    <command>faToTwoBit '$input' '$output'</command>
     <inputs>
         <param name="input" type="data" format="fasta" label="Fasta file"/>
     </inputs>
diff --git a/lib/galaxy/datatypes/converters/fasta_to_bowtie_base_index_converter.xml b/lib/galaxy/datatypes/converters/fasta_to_bowtie_base_index_converter.xml
index e1917c1a618..981e0653447 100644
--- a/lib/galaxy/datatypes/converters/fasta_to_bowtie_base_index_converter.xml
+++ b/lib/galaxy/datatypes/converters/fasta_to_bowtie_base_index_converter.xml
@@ -6,10 +6,10 @@
       <requirement type="package">bowtie</requirement>
   </requirements>
   <command>
-  mkdir ${output.files_path}
+  mkdir '${output.files_path}'
   &amp;&amp; bowtie-build --quiet
   -f 
-  $input  ${output.files_path}/${output.metadata.base_name}
+  '$input'  '${output.files_path}/${output.metadata.base_name}'
   </command>
   <inputs>
     <param name="input" type="data" format="fasta" label="Fasta file"/>
diff --git a/lib/galaxy/datatypes/converters/fasta_to_bowtie_color_index_converter.xml b/lib/galaxy/datatypes/converters/fasta_to_bowtie_color_index_converter.xml
index f34c623d97c..12df6ac519d 100644
--- a/lib/galaxy/datatypes/converters/fasta_to_bowtie_color_index_converter.xml
+++ b/lib/galaxy/datatypes/converters/fasta_to_bowtie_color_index_converter.xml
@@ -6,11 +6,11 @@
       <requirement type="package">bowtie</requirement>
   </requirements>
   <command>
-  mkdir ${output.files_path}
+  mkdir '${output.files_path}'
   &amp;&amp; bowtie-build --quiet
   --color
   -f 
-  $input  ${output.files_path}/${output.metadata.base_name}
+  '$input'  '${output.files_path}/${output.metadata.base_name}'
   </command>
   <inputs>
     <param name="input" type="data" format="fasta" label="Fasta file"/>
diff --git a/lib/galaxy/datatypes/converters/fasta_to_len.xml b/lib/galaxy/datatypes/converters/fasta_to_len.xml
index 8e1a1a0b966..159114f1cf9 100644
--- a/lib/galaxy/datatypes/converters/fasta_to_len.xml
+++ b/lib/galaxy/datatypes/converters/fasta_to_len.xml
@@ -1,7 +1,7 @@
 <tool id="CONVERTER_fasta_to_len" name="Convert FASTA to len file" version="1.0.0">
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
     <!-- Used on the metadata edit page. -->
-    <command interpreter="python">fasta_to_len.py $input $output 0</command>
+    <command interpreter="python">fasta_to_len.py '$input' '$output' 0</command>
     <inputs>
         <param name="input" type="data" format="fasta" label="Fasta file"/>
     </inputs>
diff --git a/lib/galaxy/datatypes/converters/fasta_to_tabular_converter.xml b/lib/galaxy/datatypes/converters/fasta_to_tabular_converter.xml
index 05c0b48c09a..9769e8edeb4 100644
--- a/lib/galaxy/datatypes/converters/fasta_to_tabular_converter.xml
+++ b/lib/galaxy/datatypes/converters/fasta_to_tabular_converter.xml
@@ -1,7 +1,7 @@
 <tool id="CONVERTER_fasta_to_tabular" name="Convert FASTA to Tabular" version="1.0.1">
   <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
   <!-- Used on the metadata edit page. -->
-  <command interpreter="python">fasta_to_tabular_converter.py "$input" "$output"</command>
+  <command interpreter="python">fasta_to_tabular_converter.py '$input' '$output'</command>
   <inputs>
     <param name="input" type="data" format="fasta" label="Fasta file"/>
   </inputs>
diff --git a/lib/galaxy/datatypes/converters/fastq_to_fqtoc.xml b/lib/galaxy/datatypes/converters/fastq_to_fqtoc.xml
index cf1d2f3ad11..1bf4dc33882 100644
--- a/lib/galaxy/datatypes/converters/fastq_to_fqtoc.xml
+++ b/lib/galaxy/datatypes/converters/fastq_to_fqtoc.xml
@@ -1,5 +1,5 @@
 <tool id="CONVERTER_fastq_to_fqtoc0" name="Convert FASTQ files to seek locations" version="1.0.0" hidden="true">
-  <command interpreter="python">fastq_to_fqtoc.py $input1 $output1</command>
+  <command interpreter="python">fastq_to_fqtoc.py '$input1' '$output1'</command>
   <inputs>
     <page>
         <param format="fastq" name="input1" type="data" label="Choose FASTQ file"/>
diff --git a/lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.xml b/lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.xml
index 34f41a78cfe..eaa652dcf54 100644
--- a/lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.xml
+++ b/lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.xml
@@ -1,6 +1,6 @@
 <tool id="CONVERTER_fastqsolexa_to_fasta_0" name="Convert Fastqsolexa to Fasta" version="1.0.0">
   <description>converts Fastqsolexa file to Fasta format</description>
-  <command interpreter="python">fastqsolexa_to_fasta_converter.py $input $output</command>
+  <command interpreter="python">fastqsolexa_to_fasta_converter.py '$input' '$output'</command>
   <inputs>
     <param name="input" type="data" format="fastqsolexa" label="Choose Fastqsolexa file"/>
   </inputs>
diff --git a/lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.xml b/lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.xml
index c8c8c48147a..a744009cae2 100644
--- a/lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.xml
+++ b/lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.xml
@@ -1,5 +1,5 @@
 <tool id="CONVERTER_fastqsolexa_to_qual_0" name="Convert Fastqsolexa to Qual">
-  <command interpreter="python">fastqsolexa_to_qual_converter.py $input1 $output1 ${input1.extension}</command>
+  <command interpreter="python">fastqsolexa_to_qual_converter.py '$input1' '$output1' ${input1.extension}</command>
   <inputs>
     <param format="fastqsolexa" name="input1" type="data" label="Choose Fastqsolexa file"/>
   </inputs>
diff --git a/lib/galaxy/datatypes/converters/gff_to_bed_converter.xml b/lib/galaxy/datatypes/converters/gff_to_bed_converter.xml
index 5047dd0a24c..21cbf5af25e 100644
--- a/lib/galaxy/datatypes/converters/gff_to_bed_converter.xml
+++ b/lib/galaxy/datatypes/converters/gff_to_bed_converter.xml
@@ -1,7 +1,7 @@
 <tool id="CONVERTER_gff_to_bed_0" name="Convert GFF to BED">
   <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
   <!-- Used on the metadata edit page. -->
-  <command interpreter="python">gff_to_bed_converter.py $input1 $output1</command>
+  <command interpreter="python">gff_to_bed_converter.py '$input1' '$output1'</command>
   <inputs>
     <param format="gff" name="input1" type="data" label="Choose GFF file"/>
   </inputs>
diff --git a/lib/galaxy/datatypes/converters/gff_to_bgzip_converter.xml b/lib/galaxy/datatypes/converters/gff_to_bgzip_converter.xml
index 7bea9fdd1b8..eefdcedbc3b 100644
--- a/lib/galaxy/datatypes/converters/gff_to_bgzip_converter.xml
+++ b/lib/galaxy/datatypes/converters/gff_to_bgzip_converter.xml
@@ -1,6 +1,6 @@
 <tool id="CONVERTER_gff_to_bgzip_0" name="Convert GFF to BGZIP" version="1.0.0" hidden="true">
 <!--  <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
-  <command interpreter="python">bgzip.py -P gff $input1 $output1</command>
+  <command interpreter="python">bgzip.py -P gff '$input1' '$output1'</command>
   <inputs>
     <page>
         <param format="gff" name="input1" type="data" label="Choose GFF file"/>
diff --git a/lib/galaxy/datatypes/converters/gff_to_fli_converter.xml b/lib/galaxy/datatypes/converters/gff_to_fli_converter.xml
index 14850ed80e0..ecdd6f6ae89 100644
--- a/lib/galaxy/datatypes/converters/gff_to_fli_converter.xml
+++ b/lib/galaxy/datatypes/converters/gff_to_fli_converter.xml
@@ -1,7 +1,7 @@
 <tool id="CONVERTER_gff_to_fli_0" name="Convert GFF to Feature Location Index">
   <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
   <!-- Used on the metadata edit page. -->
-  <command interpreter="python">interval_to_fli.py -F $input1.extension $input1 $output1</command>
+  <command interpreter="python">interval_to_fli.py -F $input1.extension '$input1' '$output1'</command>
   <inputs>
     <param format="gff" name="input1" type="data" label="Choose GFF file"/>
   </inputs>
diff --git a/lib/galaxy/datatypes/converters/gff_to_interval_index_converter.xml b/lib/galaxy/datatypes/converters/gff_to_interval_index_converter.xml
index a593ed6970f..63c8ba4a91b 100644
--- a/lib/galaxy/datatypes/converters/gff_to_interval_index_converter.xml
+++ b/lib/galaxy/datatypes/converters/gff_to_interval_index_converter.xml
@@ -1,6 +1,6 @@
 <tool id="CONVERTER_gff_to_interval_index_0" name="Convert GFF to Interval Index" version="1.0.0" hidden="true">
 <!--  <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
-  <command interpreter="python">gff_to_interval_index_converter.py $input1 $output1</command>
+  <command interpreter="python">gff_to_interval_index_converter.py '$input1' '$output1'</command>
   <inputs>
     <page>
         <param format="gff" name="input1" type="data" label="Choose GFF file"/>
diff --git a/lib/galaxy/datatypes/converters/gff_to_tabix_converter.xml b/lib/galaxy/datatypes/converters/gff_to_tabix_converter.xml
index e836ccd8b62..fac5dc9447d 100644
--- a/lib/galaxy/datatypes/converters/gff_to_tabix_converter.xml
+++ b/lib/galaxy/datatypes/converters/gff_to_tabix_converter.xml
@@ -1,6 +1,6 @@
 <tool id="CONVERTER_gff_to_tabix_0" name="Convert GFF to tabix" version="1.0.0" hidden="true">
 <!--  <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
-  <command interpreter="python">interval_to_tabix_converter.py -P gff $input1 $bgzip $output1</command>
+  <command interpreter="python">interval_to_tabix_converter.py -P gff '$input1' '$bgzip' '$output1'</command>
   <inputs>
     <page>
         <param format="gff" name="input1" type="data" label="Choose GFF file"/>
diff --git a/lib/galaxy/datatypes/converters/inchi_to_cml_converter.xml b/lib/galaxy/datatypes/converters/inchi_to_cml_converter.xml
index ab1db9455cc..97d751af5fe 100644
--- a/lib/galaxy/datatypes/converters/inchi_to_cml_converter.xml
+++ b/lib/galaxy/datatypes/converters/inchi_to_cml_converter.xml
@@ -6,7 +6,7 @@
     </requirements>
     <command>
 <![CDATA[
-        obabel -iinchi "${input}" -ocml -O "${output}" -e 2>&1
+        obabel -iinchi '${input}' -ocml -O '${output}' -e 2>&1
 ]]>
     </command>
     <inputs>
diff --git a/lib/galaxy/datatypes/converters/inchi_to_mol2_converter.xml b/lib/galaxy/datatypes/converters/inchi_to_mol2_converter.xml
index e7fbefb1d6e..6efe9d38ecd 100644
--- a/lib/galaxy/datatypes/converters/inchi_to_mol2_converter.xml
+++ b/lib/galaxy/datatypes/converters/inchi_to_mol2_converter.xml
@@ -6,7 +6,7 @@
     </requirements>
     <command>
 <![CDATA[
-        obabel -iinchi "${input}" -omol2 -O "${output}" -e 2>&1
+        obabel -iinchi '${input}' -omol2 -O '${output}' -e 2>&1
 ]]>
     </command>
     <inputs>
diff --git a/lib/galaxy/datatypes/converters/inchi_to_mol_converter.xml b/lib/galaxy/datatypes/converters/inchi_to_mol_converter.xml
index bc6b2e69f99..6d182178f3c 100644
--- a/lib/galaxy/datatypes/converters/inchi_to_mol_converter.xml
+++ b/lib/galaxy/datatypes/converters/inchi_to_mol_converter.xml
@@ -6,7 +6,7 @@
     </requirements>
     <command>
 <![CDATA[
-        obabel -iinchi "${input}" -omol -O "${output}" -e 2>&1
+        obabel -iinchi '${input}' -omol -O '${output}' -e 2>&1
 ]]>
     </command>
     <inputs>
diff --git a/lib/galaxy/datatypes/converters/inchi_to_sdf_converter.xml b/lib/galaxy/datatypes/converters/inchi_to_sdf_converter.xml
index 5a2c3d238cb..417fd12e906 100644
--- a/lib/galaxy/datatypes/converters/inchi_to_sdf_converter.xml
+++ b/lib/galaxy/datatypes/converters/inchi_to_sdf_converter.xml
@@ -6,7 +6,7 @@
     </requirements>
     <command>
 <![CDATA[
-        obabel -iinchi "${input}" -osdf -O "${output}" -e 2>&1
+        obabel -iinchi '${input}' -osdf -O '${output}' -e 2>&1
 ]]>
     </command>
     <inputs>
diff --git a/lib/galaxy/datatypes/converters/inchi_to_smi_converter.xml b/lib/galaxy/datatypes/converters/inchi_to_smi_converter.xml
index 87d75ca2513..b934c44604f 100644
--- a/lib/galaxy/datatypes/converters/inchi_to_smi_converter.xml
+++ b/lib/galaxy/datatypes/converters/inchi_to_smi_converter.xml
@@ -6,7 +6,7 @@
     </requirements>
     <command>
 <![CDATA[
-        obabel -iinchi "${input}" -osmi -O "${output}" -e 2>&1
+        obabel -iinchi '${input}' -osmi -O '${output}' -e 2>&1
 ]]>
     </command>
     <inputs>
diff --git a/lib/galaxy/datatypes/converters/interval_to_bed12_converter.xml b/lib/galaxy/datatypes/converters/interval_to_bed12_converter.xml
index 7e1f96b4dce..ff6a060cf14 100644
--- a/lib/galaxy/datatypes/converters/interval_to_bed12_converter.xml
+++ b/lib/galaxy/datatypes/converters/interval_to_bed12_converter.xml
@@ -1,7 +1,7 @@
 <tool id="CONVERTER_interval_to_bed12_0" name="Convert Genomic Intervals To Strict BED12">
   <!--  <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
   <!-- Used on the metadata edit page. -->
-  <command interpreter="python">interval_to_bedstrict_converter.py $output1 $input1 ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} ${input1.metadata.strandCol} ${input1.metadata.nameCol} ${input1.extension} 12</command>
+  <command interpreter="python">interval_to_bedstrict_converter.py '$output1' '$input1' ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} ${input1.metadata.strandCol} ${input1.metadata.nameCol} ${input1.extension} 12</command>
   <inputs>
     <page>
       <param format="interval" name="input1" type="data" label="Choose intervals"/>
diff --git a/lib/galaxy/datatypes/converters/interval_to_bed6_converter.xml b/lib/galaxy/datatypes/converters/interval_to_bed6_converter.xml
index 0353fb93efe..c992a63db9e 100644
--- a/lib/galaxy/datatypes/converters/interval_to_bed6_converter.xml
+++ b/lib/galaxy/datatypes/converters/interval_to_bed6_converter.xml
@@ -1,7 +1,7 @@
 <tool id="CONVERTER_interval_to_bed6_0" name="Convert Genomic Intervals To Strict BED6">
   <!--  <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
   <!-- Used on the metadata edit page. -->
-  <command interpreter="python">interval_to_bedstrict_converter.py $output1 $input1 ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} ${input1.metadata.strandCol} ${input1.metadata.nameCol} ${input1.extension} 6</command>
+  <command interpreter="python">interval_to_bedstrict_converter.py '$output1' '$input1' ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} ${input1.metadata.strandCol} ${input1.metadata.nameCol} ${input1.extension} 6</command>
   <inputs>
     <page>
       <param format="interval" name="input1" type="data" label="Choose intervals"/>
diff --git a/lib/galaxy/datatypes/converters/interval_to_bed_converter.xml b/lib/galaxy/datatypes/converters/interval_to_bed_converter.xml
index acbf20b920d..1e46eeff47f 100644
--- a/lib/galaxy/datatypes/converters/interval_to_bed_converter.xml
+++ b/lib/galaxy/datatypes/converters/interval_to_bed_converter.xml
@@ -1,7 +1,7 @@
 <tool id="CONVERTER_interval_to_bed_0" name="Convert Genomic Intervals To BED">
   <!--  <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
   <!-- Used on the metadata edit page. -->
-  <command interpreter="python">interval_to_bed_converter.py $output1 $input1 ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} ${input1.metadata.strandCol} ${input1.metadata.nameCol}</command>
+  <command interpreter="python">interval_to_bed_converter.py '$output1' '$input1' ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} ${input1.metadata.strandCol} ${input1.metadata.nameCol}</command>
   <inputs>
     <page>
       <param format="interval" name="input1" type="data" label="Choose intervals"/>
diff --git a/lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.xml b/lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.xml
index 39ed10e5711..79e919ab9e8 100644
--- a/lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.xml
+++ b/lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.xml
@@ -1,7 +1,7 @@
 <tool id="CONVERTER_interval_to_bedstrict_0" name="Convert Genomic Intervals To Strict BED">
   <!--  <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
   <!-- Used on the metadata edit page. -->
-  <command interpreter="python">interval_to_bedstrict_converter.py $output1 $input1 ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} ${input1.metadata.strandCol} ${input1.metadata.nameCol} ${input1.extension}</command>
+  <command interpreter="python">interval_to_bedstrict_converter.py '$output1' '$input1' ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} ${input1.metadata.strandCol} ${input1.metadata.nameCol} ${input1.extension}</command>
   <inputs>
     <page>
       <param format="interval" name="input1" type="data" label="Choose intervals"/>
diff --git a/lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml b/lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml
index 720f9fb17ab..11eb5a9240b 100644
--- a/lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml
+++ b/lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml
@@ -4,7 +4,7 @@
                                   -c ${input1.metadata.chromCol} 
                                   -s ${input1.metadata.startCol} 
                                   -e ${input1.metadata.endCol} 
-                                  $input1 $output1
+                                  '$input1' '$output1'
   </command>
   <inputs>
     <page>
diff --git a/lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml b/lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml
index 7459bfd4329..7ead71aacb3 100644
--- a/lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml
+++ b/lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml
@@ -8,7 +8,7 @@
   <command>
 
     ## Remove comments and sort by chromosome.
-    grep -v '^#' $input1 | sort -k${input1.metadata.chromCol},${input1.metadata.chromCol} |
+    grep -v '^#' '$input1' | sort -k${input1.metadata.chromCol},${input1.metadata.chromCol} |
 
     ## Create simple BED by cutting chrom, start, and end columns.
     awk -v OFS='	' '{print $${input1.metadata.chromCol},$${input1.metadata.startCol},$${input1.metadata.endCol} }' |
@@ -18,10 +18,10 @@
 
     ## Streaming the bedgraph file to wigToBigWig is fast but very memory intensive; hence, this
     ## should only be used on systems with large RAM.
-    ## | wigToBigWig stdin $chromInfo $output
+    ## | wigToBigWig stdin $chromInfo '$output'
 
     ## This can be used anywhere.
-    > temp.bg ; bedGraphToBigWig temp.bg $chromInfo $output
+    > temp.bg ; bedGraphToBigWig temp.bg $chromInfo '$output'
 
   </command>
   <inputs>
diff --git a/lib/galaxy/datatypes/converters/interval_to_coverage.xml b/lib/galaxy/datatypes/converters/interval_to_coverage.xml
index 3ad64f7b9ba..7bd21c161e2 100644
--- a/lib/galaxy/datatypes/converters/interval_to_coverage.xml
+++ b/lib/galaxy/datatypes/converters/interval_to_coverage.xml
@@ -1,7 +1,7 @@
 <tool id="CONVERTER_interval_to_coverage_0" name="Convert Genomic Intervals To COVERAGE">
   <!--  <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
   <!-- Used on the metadata edit page. -->
-  <command interpreter="python">interval_to_coverage.py $input1 $output1 
+  <command interpreter="python">interval_to_coverage.py '$input1' '$output1'
   -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol}
   -2 ${output1.metadata.chromCol},${output1.metadata.positionCol},${output1.metadata.forwardCol},${output1.metadata.reverseCol}
   </command>
diff --git a/lib/galaxy/datatypes/converters/interval_to_interval_index_converter.xml b/lib/galaxy/datatypes/converters/interval_to_interval_index_converter.xml
index 19917be0816..c69f337e3b5 100644
--- a/lib/galaxy/datatypes/converters/interval_to_interval_index_converter.xml
+++ b/lib/galaxy/datatypes/converters/interval_to_interval_index_converter.xml
@@ -4,7 +4,7 @@
                                 -c ${input1.metadata.chromCol} 
                                 -s ${input1.metadata.startCol} 
                                 -e ${input1.metadata.endCol} 
-                                $input1 $output1
+                                '$input1' '$output1'
   </command>
   <inputs>
     <page>
diff --git a/lib/galaxy/datatypes/converters/interval_to_tabix_converter.xml b/lib/galaxy/datatypes/converters/interval_to_tabix_converter.xml
index 454bbfdb092..1dc6ddedf77 100644
--- a/lib/galaxy/datatypes/converters/interval_to_tabix_converter.xml
+++ b/lib/galaxy/datatypes/converters/interval_to_tabix_converter.xml
@@ -4,7 +4,7 @@
                                   -c ${input1.metadata.chromCol} 
                                   -s ${input1.metadata.startCol} 
                                   -e ${input1.metadata.endCol} 
-                                  $input1 $bgzip $output1    
+                                  '$input1' '$bgzip' '$output1'
   </command>
   <inputs>
     <page>
diff --git a/lib/galaxy/datatypes/converters/len_to_linecount.xml b/lib/galaxy/datatypes/converters/len_to_linecount.xml
index 9a91d8723b8..3398fa4a821 100644
--- a/lib/galaxy/datatypes/converters/len_to_linecount.xml
+++ b/lib/galaxy/datatypes/converters/len_to_linecount.xml
@@ -1,7 +1,7 @@
 <tool id="CONVERTER_len_to_linecount" name="Convert Len file to Linecount" version="1.0.0">
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
     <!-- Used on the metadata edit page. -->
-    <command>wc -l $input | awk '{print $1}' &gt; $output </command>
+    <command>wc -l '$input' | awk '{print $1}' &gt; '$output' </command>
     <inputs>
         <param name="input" type="data" format="len" label="Fasta file"/>
     </inputs>
diff --git a/lib/galaxy/datatypes/converters/maf_to_fasta_converter.xml b/lib/galaxy/datatypes/converters/maf_to_fasta_converter.xml
index 643a94ef75c..fcb6ef21247 100644
--- a/lib/galaxy/datatypes/converters/maf_to_fasta_converter.xml
+++ b/lib/galaxy/datatypes/converters/maf_to_fasta_converter.xml
@@ -1,6 +1,6 @@
 <tool id="CONVERTER_maf_to_fasta_0" name="Convert MAF to Fasta" version="1.0.1">
 <!--  <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
-  <command interpreter="python">maf_to_fasta_converter.py $output1 $input1</command>
+  <command interpreter="python">maf_to_fasta_converter.py '$output1' '$input1'</command>
   <inputs>
     <page>
         <param format="maf" name="input1" type="data" label="Choose MAF file"/>
diff --git a/lib/galaxy/datatypes/converters/maf_to_interval_converter.xml b/lib/galaxy/datatypes/converters/maf_to_interval_converter.xml
index 17220e9a1f0..6e85eaa34f9 100644
--- a/lib/galaxy/datatypes/converters/maf_to_interval_converter.xml
+++ b/lib/galaxy/datatypes/converters/maf_to_interval_converter.xml
@@ -1,6 +1,6 @@
 <tool id="CONVERTER_maf_to_interval_0" name="Convert MAF to Genomic Intervals" version="1.0.2">
 <!--  <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
-  <command interpreter="python">maf_to_interval_converter.py $output1 $input1 ${input1.metadata.dbkey}</command>
+  <command interpreter="python">maf_to_interval_converter.py '$output1' '$input1' '${input1.metadata.dbkey}'</command>
   <inputs>
     <page>
         <param format="maf" name="input1" type="data" label="Choose MAF file"/>
diff --git a/lib/galaxy/datatypes/converters/mol2_to_cml_converter.xml b/lib/galaxy/datatypes/converters/mol2_to_cml_converter.xml
index ab040297baf..24b5f60d7e2 100644
--- a/lib/galaxy/datatypes/converters/mol2_to_cml_converter.xml
+++ b/lib/galaxy/datatypes/converters/mol2_to_cml_converter.xml
@@ -6,7 +6,7 @@
     </requirements>
     <command>
 <![CDATA[
-        obabel -imol2 "${input}" -ocml -O "${output}" -e 2>&1
+        obabel -imol2 '${input}' -ocml -O '${output}' -e 2>&1
 ]]>
     </command>
     <inputs>
diff --git a/lib/galaxy/datatypes/converters/mol2_to_inchi_converter.xml b/lib/galaxy/datatypes/converters/mol2_to_inchi_converter.xml
index a1215816505..be5daa3e882 100644
--- a/lib/galaxy/datatypes/converters/mol2_to_inchi_converter.xml
+++ b/lib/galaxy/datatypes/converters/mol2_to_inchi_converter.xml
@@ -6,7 +6,7 @@
     </requirements>
     <command>
 <![CDATA[
-        obabel -imol2 "${input}" -oinchi -O "${output}" -e 2>&1
+        obabel -imol2 '${input}' -oinchi -O '${output}' -e 2>&1
 ]]>
     </command>
     <inputs>
diff --git a/lib/galaxy/datatypes/converters/mol2_to_mol_converter.xml b/lib/galaxy/datatypes/converters/mol2_to_mol_converter.xml
index 75b88369892..e1210058cb0 100644
--- a/lib/galaxy/datatypes/converters/mol2_to_mol_converter.xml
+++ b/lib/galaxy/datatypes/converters/mol2_to_mol_converter.xml
@@ -6,7 +6,7 @@
     </requirements>
     <command>
 <![CDATA[
-        obabel -imol2 "${input}" -omol -O "${output}" -e 2>&1
+        obabel -imol2 '${input}' -omol -O '${output}' -e 2>&1
 ]]>
     </command>
     <inputs>
diff --git a/lib/galaxy/datatypes/converters/mol2_to_sdf_converter.xml b/lib/galaxy/datatypes/converters/mol2_to_sdf_converter.xml
index 9bd01e9afb5..e72b17ebe1a 100644
--- a/lib/galaxy/datatypes/converters/mol2_to_sdf_converter.xml
+++ b/lib/galaxy/datatypes/converters/mol2_to_sdf_converter.xml
@@ -6,7 +6,7 @@
     </requirements>
     <command>
 <![CDATA[
-        obabel -imol2 "${input}" -osdf "${output}" -e 2>&1
+        obabel -imol2 '${input}' -osdf '${output}' -e 2>&1
 ]]>
     </command>
     <inputs>
diff --git a/lib/galaxy/datatypes/converters/mol2_to_smi_converter.xml b/lib/galaxy/datatypes/converters/mol2_to_smi_converter.xml
index 05fac1f3f2a..c8f30d0c0d5 100644
--- a/lib/galaxy/datatypes/converters/mol2_to_smi_converter.xml
+++ b/lib/galaxy/datatypes/converters/mol2_to_smi_converter.xml
@@ -6,7 +6,7 @@
     </requirements>
     <command>
 <![CDATA[
-        obabel -imol2 "${input}" -omol "${output}" -e 2>&1
+        obabel -imol2 '${input}' -omol '${output}' -e 2>&1
 ]]>
     </command>
     <inputs>
diff --git a/lib/galaxy/datatypes/converters/mol_to_cml_converter.xml b/lib/galaxy/datatypes/converters/mol_to_cml_converter.xml
index 1af29c63fc3..a13979d8eef 100644
--- a/lib/galaxy/datatypes/converters/mol_to_cml_converter.xml
+++ b/lib/galaxy/datatypes/converters/mol_to_cml_converter.xml
@@ -5,7 +5,7 @@
     </requirements>
     <command>
 <![CDATA[
-        obabel -imol "${input}" -ocml -O "${output}" -e 2>&1
+        obabel -imol '${input}' -ocml -O '${output}' -e 2>&1
 ]]>
     </command>
     <inputs>
diff --git a/lib/galaxy/datatypes/converters/mol_to_inchi_converter.xml b/lib/galaxy/datatypes/converters/mol_to_inchi_converter.xml
index 185e8337815..e14263e7b2e 100644
--- a/lib/galaxy/datatypes/converters/mol_to_inchi_converter.xml
+++ b/lib/galaxy/datatypes/converters/mol_to_inchi_converter.xml
@@ -5,7 +5,7 @@
     </requirements>
     <command>
 <![CDATA[
-        obabel -imol "${input}" -omol2 -O "${output}" -e 2>&1
+        obabel -imol '${input}' -omol2 -O '${output}' -e 2>&1
 ]]>
     </command>
     <inputs>
diff --git a/lib/galaxy/datatypes/converters/mol_to_mol2_converter.xml b/lib/galaxy/datatypes/converters/mol_to_mol2_converter.xml
index 185e8337815..e14263e7b2e 100644
--- a/lib/galaxy/datatypes/converters/mol_to_mol2_converter.xml
+++ b/lib/galaxy/datatypes/converters/mol_to_mol2_converter.xml
@@ -5,7 +5,7 @@
     </requirements>
     <command>
 <![CDATA[
-        obabel -imol "${input}" -omol2 -O "${output}" -e 2>&1
+        obabel -imol '${input}' -omol2 -O '${output}' -e 2>&1
 ]]>
     </command>
     <inputs>
diff --git a/lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.xml b/lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.xml
index 120eb641624..5ed6cac1195 100644
--- a/lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.xml
+++ b/lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.xml
@@ -1,6 +1,6 @@
 <tool id="CONVERTER_picard_interval_list_to_bed6" name="Convert Picard Interval List to BED6" version="1.0.0">
     <description>converter</description>
-    <command interpreter="python">picard_interval_list_to_bed6_converter.py "$input" "$output"</command>
+    <command interpreter="python">picard_interval_list_to_bed6_converter.py '$input' '$output'</command>
     <inputs>
         <param name="input" type="data" format="picard_interval_list" label="Picard Interval List file"/>
     </inputs>
diff --git a/lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.xml b/lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.xml
index f0c507e784c..50436711114 100644
--- a/lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.xml
+++ b/lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.xml
@@ -1,6 +1,6 @@
 <tool id="CONVERTER_pileup_to_interval_index_0" name="Convert Pileup to Interval Index" version="1.0.0" hidden="true">
 <!--  <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
-  <command interpreter="python">pileup_to_interval_index_converter.py $input $output
+  <command interpreter="python">pileup_to_interval_index_converter.py '$input' '$output'
   </command>
   <inputs>
     <page>
diff --git a/lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.xml b/lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.xml
index 337d07815b6..2d1d9db87ed 100644
--- a/lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.xml
+++ b/lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.xml
@@ -1,6 +1,6 @@
 <tool id="CONVERTER_ref_to_seq_taxomony" name="Convert Ref taxonomy to Seq Taxonomy" version="1.0.0">
   <description>converts 2 or 3 column sequence taxonomy file to a 2 column mothur taxonomy_outline format</description>
-  <command> python $__tool_directory__/ref_to_seq_taxonomy_converter.py "$input" "$output"</command>
+  <command> python '$__tool_directory__/ref_to_seq_taxonomy_converter.py' '$input' '$output'</command>
   <inputs>
     <param name="input" type="data" format="mothur.ref.taxonomy" label="a Sequence Taxomony file"/>
   </inputs>
diff --git a/lib/galaxy/datatypes/converters/sam_to_bam.xml b/lib/galaxy/datatypes/converters/sam_to_bam.xml
index 8d743d8ad7a..67636c5a411 100644
--- a/lib/galaxy/datatypes/converters/sam_to_bam.xml
+++ b/lib/galaxy/datatypes/converters/sam_to_bam.xml
@@ -8,7 +8,7 @@
     <requirements>
         <requirement type="package">samtools</requirement>
     </requirements>
-    <command interpreter="python">sam_to_bam.py $input1 $output</command>
+    <command interpreter="python">sam_to_bam.py '$input1' '$output'</command>
     <inputs>
         <param name="input1" type="data" format="sam" label="SAM file"/>
     </inputs>
diff --git a/lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml b/lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml
index 9bc7219ff04..2465aeafcb6 100644
--- a/lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml
+++ b/lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml
@@ -5,14 +5,14 @@
         <requirement type="package">bedtools</requirement>
     </requirements>
     <command>
-        samtools view -bh $input | bedtools genomecov -bg -split -ibam stdin -g $chromInfo 
+        samtools view -bh '$input' | bedtools genomecov -bg -split -ibam stdin -g $chromInfo
 
         ## Streaming the bedgraph file to wigToBigWig is fast but very memory intensive; hence, this
         ## should only be used on systems with large RAM.
-        ## | wigToBigWig stdin $chromInfo $output
+        ## | wigToBigWig stdin $chromInfo '$output'
 
         ## This can be used anywhere.
-        > temp.bg ; bedGraphToBigWig temp.bg $chromInfo $output
+        > temp.bg ; bedGraphToBigWig temp.bg $chromInfo '$output'
     </command>
     <inputs>
         <param format="bam" name="input" type="data" label="Choose BAM file"/>
diff --git a/lib/galaxy/datatypes/converters/sdf_to_cml_converter.xml b/lib/galaxy/datatypes/converters/sdf_to_cml_converter.xml
index 0d63fe47427..62cf3074c0a 100644
--- a/lib/galaxy/datatypes/converters/sdf_to_cml_converter.xml
+++ b/lib/galaxy/datatypes/converters/sdf_to_cml_converter.xml
@@ -6,7 +6,7 @@
     </requirements>
     <command>
 <![CDATA[
-        obabel -isdf "${input}" -ocml -O "${output}" -e 2>&1
+        obabel -isdf '${input}' -ocml -O '${output}' -e 2>&1
 ]]>
     </command>
     <inputs>
diff --git a/lib/galaxy/datatypes/converters/sdf_to_inchi_converter.xml b/lib/galaxy/datatypes/converters/sdf_to_inchi_converter.xml
index 1d78781f00b..af588740733 100644
--- a/lib/galaxy/datatypes/converters/sdf_to_inchi_converter.xml
+++ b/lib/galaxy/datatypes/converters/sdf_to_inchi_converter.xml
@@ -6,7 +6,7 @@
     </requirements>
     <command>
 <![CDATA[
-        obabel -isdf "${input}" -oinchi -O "${output}" -e 2>&1
+        obabel -isdf '${input}' -oinchi -O '${output}' -e 2>&1
 ]]>
     </command>
     <inputs>
diff --git a/lib/galaxy/datatypes/converters/sdf_to_mol2_converter.xml b/lib/galaxy/datatypes/converters/sdf_to_mol2_converter.xml
index ac326e239d6..3d0aac2b261 100644
--- a/lib/galaxy/datatypes/converters/sdf_to_mol2_converter.xml
+++ b/lib/galaxy/datatypes/converters/sdf_to_mol2_converter.xml
@@ -6,7 +6,7 @@
     </requirements>
     <command>
 <![CDATA[
-        obabel -isdf "${input}" -omol2 -O "${output}" -e 2>&1
+        obabel -isdf '${input}' -omol2 -O '${output}' -e 2>&1
 ]]>
     </command>
     <inputs>
diff --git a/lib/galaxy/datatypes/converters/sdf_to_smi_converter.xml b/lib/galaxy/datatypes/converters/sdf_to_smi_converter.xml
index f157f799c02..a2b5402c513 100644
--- a/lib/galaxy/datatypes/converters/sdf_to_smi_converter.xml
+++ b/lib/galaxy/datatypes/converters/sdf_to_smi_converter.xml
@@ -7,9 +7,9 @@
     <command >
 <![CDATA[
         obabel
-            -isdf "${input}"
+            -isdf '${input}'
             -ocan
-            -O "${output}"
+            -O '${output}'
             -e
         2>&1
 ]]>
diff --git a/lib/galaxy/datatypes/converters/smi_to_cml_converter.xml b/lib/galaxy/datatypes/converters/smi_to_cml_converter.xml
index 0ab97693d2b..1a1302d3a0e 100644
--- a/lib/galaxy/datatypes/converters/smi_to_cml_converter.xml
+++ b/lib/galaxy/datatypes/converters/smi_to_cml_converter.xml
@@ -6,7 +6,7 @@
     </requirements>
     <command>
 <![CDATA[
-        obabel -ismi "${input}" -ocml -O "${output}" -e 2>&1
+        obabel -ismi '${input}' -ocml -O '${output}' -e 2>&1
 ]]>
     </command>
     <inputs>
diff --git a/lib/galaxy/datatypes/converters/smi_to_inchi_converter.xml b/lib/galaxy/datatypes/converters/smi_to_inchi_converter.xml
index 75de06cbeb9..7a80c501146 100644
--- a/lib/galaxy/datatypes/converters/smi_to_inchi_converter.xml
+++ b/lib/galaxy/datatypes/converters/smi_to_inchi_converter.xml
@@ -6,7 +6,7 @@
     </requirements>
     <command>
 <![CDATA[
-        obabel -ismi "${input}" -oinchi -O "${output}" -e 2>&1
+        obabel -ismi '${input}' -oinchi -O '${output}' -e 2>&1
 ]]>
     </command>
     <inputs>
diff --git a/lib/galaxy/datatypes/converters/smi_to_mol2_converter.xml b/lib/galaxy/datatypes/converters/smi_to_mol2_converter.xml
index df068cace6f..6542b42fce3 100644
--- a/lib/galaxy/datatypes/converters/smi_to_mol2_converter.xml
+++ b/lib/galaxy/datatypes/converters/smi_to_mol2_converter.xml
@@ -6,7 +6,7 @@
     </requirements>
     <command>
 <![CDATA[
-        obabel -ismi "${input}" -omol2 -O "${output}" -e 2>&1
+        obabel -ismi '${input}' -omol2 -O '${output}' -e 2>&1
 ]]>
     </command>
     <inputs>
diff --git a/lib/galaxy/datatypes/converters/smi_to_mol_converter.xml b/lib/galaxy/datatypes/converters/smi_to_mol_converter.xml
index c9959815b75..78ac5db970e 100644
--- a/lib/galaxy/datatypes/converters/smi_to_mol_converter.xml
+++ b/lib/galaxy/datatypes/converters/smi_to_mol_converter.xml
@@ -6,7 +6,7 @@
     </requirements>
     <command>
 <![CDATA[
-        obabel -ismi "${input}" -omol -O "${output}" -e 2>&1
+        obabel -ismi '${input}' -omol -O '${output}' -e 2>&1
 ]]>
     </command>
     <inputs>
diff --git a/lib/galaxy/datatypes/converters/smi_to_sdf_converter.xml b/lib/galaxy/datatypes/converters/smi_to_sdf_converter.xml
index f5c213dd275..a61f255bae4 100644
--- a/lib/galaxy/datatypes/converters/smi_to_sdf_converter.xml
+++ b/lib/galaxy/datatypes/converters/smi_to_sdf_converter.xml
@@ -6,7 +6,7 @@
     </requirements>
     <command>
 <![CDATA[
-    obabel -ismi "${input}" -osdf -O "${output}" -e 2>&1
+    obabel -ismi '${input}' -osdf -O '${output}' -e 2>&1
 ]]>
     </command>
     <inputs>
diff --git a/lib/galaxy/datatypes/converters/smi_to_smi_converter.xml b/lib/galaxy/datatypes/converters/smi_to_smi_converter.xml
index ce0f1ba63ed..d177053f8ed 100644
--- a/lib/galaxy/datatypes/converters/smi_to_smi_converter.xml
+++ b/lib/galaxy/datatypes/converters/smi_to_smi_converter.xml
@@ -7,13 +7,13 @@
     <command >
 <![CDATA[
         obabel
-            -ismi "${input}"
+            -ismi '${input}'
             #if $can:
                 -ocan
             #else:
                 -osmi
             #end if
-            -O "${output}"
+            -O '${output}'
             -e
             $remove_h
             #if $iso_chi or $can or $exp_h:
diff --git a/lib/galaxy/datatypes/converters/tabular_to_dbnsfp.xml b/lib/galaxy/datatypes/converters/tabular_to_dbnsfp.xml
index 84803d593e2..4e12954d91c 100644
--- a/lib/galaxy/datatypes/converters/tabular_to_dbnsfp.xml
+++ b/lib/galaxy/datatypes/converters/tabular_to_dbnsfp.xml
@@ -1,6 +1,6 @@
 <tool id="tabular_to_dbnsfp" name="Convert tabular to dbnsfp" version="1.0.0">
   <description></description> 
-  <command interpreter="python">tabular_to_dbnsfp.py $input $dbnsfp.extra_files_path/dbNSFP.gz</command>
+  <command interpreter="python">tabular_to_dbnsfp.py '$input' '$dbnsfp.extra_files_path/dbNSFP.gz'</command>
   <inputs>
       <param format="tabular" name="input" type="data" label="Choose a dbnsfp tabular file"/>
    </inputs>
diff --git a/lib/galaxy/datatypes/converters/vcf_to_bgzip_converter.xml b/lib/galaxy/datatypes/converters/vcf_to_bgzip_converter.xml
index 75316682764..944c4fa9fac 100644
--- a/lib/galaxy/datatypes/converters/vcf_to_bgzip_converter.xml
+++ b/lib/galaxy/datatypes/converters/vcf_to_bgzip_converter.xml
@@ -1,6 +1,6 @@
 <tool id="CONVERTER_vcf_to_bgzip_0" name="Convert VCF to BGZIP" version="1.0.0" hidden="true">
 <!--  <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
-  <command interpreter="python">bgzip.py -P vcf $input1 $output1</command>
+  <command interpreter="python">bgzip.py -P vcf '$input1' '$output1'</command>
   <inputs>
     <page>
         <param format="vcf" name="input1" type="data" label="Choose Vcf file"/>
diff --git a/lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.xml b/lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.xml
index 220f7e4b60b..5cd831e326f 100644
--- a/lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.xml
+++ b/lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.xml
@@ -1,6 +1,6 @@
 <tool id="CONVERTER_vcf_to_interval_index_0" name="Convert VCF to Interval Index" version="1.0.0" hidden="true">
   <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description>
-  <command interpreter="python">vcf_to_interval_index_converter.py $input1 $output1</command>
+  <command interpreter="python">vcf_to_interval_index_converter.py '$input1' '$output1'</command>
   <inputs>
     <page>
         <param format="vcf" name="input1" type="data" label="Choose VCF file"/>
diff --git a/lib/galaxy/datatypes/converters/vcf_to_tabix_converter.xml b/lib/galaxy/datatypes/converters/vcf_to_tabix_converter.xml
index 859c5749457..9d37e83d3a1 100644
--- a/lib/galaxy/datatypes/converters/vcf_to_tabix_converter.xml
+++ b/lib/galaxy/datatypes/converters/vcf_to_tabix_converter.xml
@@ -1,6 +1,6 @@
 <tool id="CONVERTER_vcf_to_tabix_0" name="Convert Vcf to tabix" version="1.0.0" hidden="true">
 <!--  <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
-  <command interpreter="python">interval_to_tabix_converter.py -P vcf $input1 $bgzip $output1</command>
+  <command interpreter="python">interval_to_tabix_converter.py -P vcf '$input1' '$bgzip' '$output1'</command>
   <inputs>
     <page>
         <param format="vcf" name="input1" type="data" label="Choose Vcf file"/>
diff --git a/lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml b/lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml
index f77b845fc25..f0d80a771b2 100644
--- a/lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml
+++ b/lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml
@@ -4,7 +4,7 @@
       <requirement type="package">ucsc_tools</requirement>
   </requirements>
   <command>
-      grep -v "^track" $input | wigToBigWig -clip stdin $chromInfo $output 
+      grep -v "^track" '$input' | wigToBigWig -clip stdin $chromInfo '$output'
       2&gt;&amp;1 || echo "Error running wiggle to bigwig converter." >&amp;2
   </command>
   <inputs>
diff --git a/lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.xml b/lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.xml
index 9fdd0b91e45..30b316c0872 100644
--- a/lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.xml
+++ b/lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.xml
@@ -1,6 +1,6 @@
 <tool id="CONVERTER_Wiggle_0" name="Index Wiggle for Track Viewer" hidden="true">
   <!-- Used internally to generate track indexes -->
-  <command interpreter="python">wiggle_to_array_tree_converter.py $input $output</command>
+  <command interpreter="python">wiggle_to_array_tree_converter.py '$input' '$output'</command>
   <inputs>
     <page>
       <param format="wiggle" name="input" type="data" label="Choose wiggle"/>
diff --git a/lib/galaxy/datatypes/converters/wiggle_to_simple_converter.xml b/lib/galaxy/datatypes/converters/wiggle_to_simple_converter.xml
index ff9a7cfe82d..1f92874827e 100644
--- a/lib/galaxy/datatypes/converters/wiggle_to_simple_converter.xml
+++ b/lib/galaxy/datatypes/converters/wiggle_to_simple_converter.xml
@@ -1,7 +1,7 @@
 <tool id="CONVERTER_wiggle_to_interval_0" name="Wiggle to Interval">
-  <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
+  <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
   <!-- Used on the metadata edit page. -->
-  <command interpreter="python">wiggle_to_simple_converter.py $input $out_file1 </command>
+  <command interpreter="python">wiggle_to_simple_converter.py '$input' '$out_file1' </command>
   <inputs>
     <param format="wig" name="input" type="data" label="Convert"/>
   </inputs>
diff --git a/lib/galaxy/tools/imp_exp/exp_history_to_archive.xml b/lib/galaxy/tools/imp_exp/exp_history_to_archive.xml
index 9b2454150ab..b1e51ff825f 100644
--- a/lib/galaxy/tools/imp_exp/exp_history_to_archive.xml
+++ b/lib/galaxy/tools/imp_exp/exp_history_to_archive.xml
@@ -1,7 +1,7 @@
 <tool id="__EXPORT_HISTORY__" name="Export History" version="0.1" tool_type="export_history">
   <type class="ExportHistoryTool" module="galaxy.tools"/>
   <action module="galaxy.tools.actions.history_imp_exp" class="ExportHistoryToolAction"/>
-  <command>python $export_history $__EXPORT_HISTORY_COMMAND_INPUTS_OPTIONS__ $output_file</command>
+  <command>python '$export_history' '$__EXPORT_HISTORY_COMMAND_INPUTS_OPTIONS__' '$output_file'</command>
   <inputs>
     <param name="__HISTORY_TO_EXPORT__" type="hidden"/>
     <param name="compress" type="boolean"/>

From 89e6f77feb4404ecb9e0ba025b5d2168e627ed71 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sat, 12 Nov 2016 13:58:54 +0100
Subject: [PATCH 2/2] Don't quote

---
 lib/galaxy/tools/imp_exp/exp_history_to_archive.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/tools/imp_exp/exp_history_to_archive.xml b/lib/galaxy/tools/imp_exp/exp_history_to_archive.xml
index b1e51ff825f..02320b18fbb 100644
--- a/lib/galaxy/tools/imp_exp/exp_history_to_archive.xml
+++ b/lib/galaxy/tools/imp_exp/exp_history_to_archive.xml
@@ -1,7 +1,7 @@
 <tool id="__EXPORT_HISTORY__" name="Export History" version="0.1" tool_type="export_history">
   <type class="ExportHistoryTool" module="galaxy.tools"/>
   <action module="galaxy.tools.actions.history_imp_exp" class="ExportHistoryToolAction"/>
-  <command>python '$export_history' '$__EXPORT_HISTORY_COMMAND_INPUTS_OPTIONS__' '$output_file'</command>
+  <command>python '$export_history' $__EXPORT_HISTORY_COMMAND_INPUTS_OPTIONS__ '$output_file'</command>
   <inputs>
     <param name="__HISTORY_TO_EXPORT__" type="hidden"/>
     <param name="compress" type="boolean"/>