Merge pull request #3165 from mvdbeek/quote_data_converters

Quote all paths in converter tool xml
2026-09-24 16:30:27 +08:00 · 2016-11-13 22:45:13 -05:00
parent 3ec7be2795 89e6f77feb
commit 46bd40bdc4
72 changed files with 82 additions and 82 deletions
@@ -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>
@@ -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>
@@ -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"/>
@@ -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"/>
@@ -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>
@@ -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>
@@ -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>
@@ -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>
@@ -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:
@@ -4,7 +4,7 @@
                                  -c ${input1.metadata.chromCol} 
                                  -s ${input1.metadata.startCol} 
                                  -e ${input1.metadata.endCol} 
-                                  $input1 $output1
+                                  '$input1' '$output1'
  </command>
  <inputs>
    <page>
@@ -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>
@@ -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>
@@ -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"/>
@@ -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"/>
@@ -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' '$output' 0</command>
    <inputs>
        <param name="input" type="data" format="fasta" label="Fasta file"/>
    </inputs>
@@ -1,7 +1,7 @@
 <tool id="CONVERTER_fasta_to_tabular" name="Convert FASTA to Tabular" version="1.0.1">
  <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
  <!-- Used on the metadata edit page. -->
-  <command interpreter="python">fasta_to_tabular_converter.py "$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>
@@ -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"/>
@@ -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>
@@ -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>
@@ -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>
@@ -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"/>
@@ -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>
@@ -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"/>
@@ -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"/>
@@ -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>
@@ -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>
@@ -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>
@@ -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>
@@ -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>
@@ -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"/>
@@ -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"/>
@@ -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"/>
@@ -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"/>
@@ -4,7 +4,7 @@
                                  -c ${input1.metadata.chromCol} 
                                  -s ${input1.metadata.startCol} 
                                  -e ${input1.metadata.endCol} 
-                                  $input1 $output1
+                                  '$input1' '$output1'
  </command>
  <inputs>
    <page>
@@ -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>
@@ -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>
@@ -4,7 +4,7 @@
                                -c ${input1.metadata.chromCol} 
                                -s ${input1.metadata.startCol} 
                                -e ${input1.metadata.endCol} 
-                                $input1 $output1
+                                '$input1' '$output1'
  </command>
  <inputs>
    <page>
@@ -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>
@@ -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>
@@ -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"/>
@@ -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"/>
@@ -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>
@@ -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>
@@ -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>
@@ -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>
@@ -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>
@@ -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>
@@ -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>
@@ -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>
@@ -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>
@@ -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>
@@ -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>
@@ -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>
@@ -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"/>
@@ -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>
@@ -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>
@@ -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>
@@ -7,9 +7,9 @@
    <command >
 <![CDATA[
        obabel
-            -isdf "${input}"
+            -isdf '${input}'
            -ocan
-            -O "${output}"
+            -O '${output}'
            -e
        2>&1
 ]]>
@@ -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>
@@ -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>
@@ -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>
@@ -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>
@@ -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>
@@ -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:
@@ -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>
@@ -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"/>
@@ -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"/>
@@ -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"/>
@@ -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>
@@ -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"/>
@@ -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>
@@ -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"/>