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Update FASTX tool wrappers to handle fastqsanger by passing -Q 33 to command-line as needed.

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This commit is contained in:
Daniel Blankenberg
2011-01-27 09:54:53 -05:00
parent ed947c6032
commit 00ddaa2dcf
10 changed files with 51 additions and 23 deletions
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tools/fastq/fastq_masker_by_quality.xml
+1 -1
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@@ -21,7 +21,7 @@
<option value="ge">Greater than</option>
<option value="gt">Greater than or equal</option>
</param>
<param name="quality_score" type="integer" value="0"/>
<param name="quality_score" type="integer" value="0" label="Quality score"/>
</inputs>
<outputs>
<data name="output_file" format="fastqsanger" />
tools/fastx_toolkit/fastq_quality_filter.xml
+7 -3
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@@ -2,7 +2,11 @@
<description></description>
<requirements><requirement type="package">fastx_toolkit</requirement></requirements>
<command>zcat -f '$input' | fastq_quality_filter -q $quality -p $percent -v -o $output</command>
<command>zcat -f '$input' | fastq_quality_filter -q $quality -p $percent -v -o $output
#if $input.ext == "fastqsanger":
-Q 33
#end if
</command>
<inputs>
<param format="fastqsolexa,fastqsanger" name="input" type="data" label="Library to filter" />
@@ -19,14 +23,14 @@
<tests>
<test>
<!-- Test1: 100% of bases with quality 33 or higher (pretty steep requirement...) -->
<param name="input" value="fastq_qual_filter1.fastq" />
<param name="input" value="fastq_qual_filter1.fastq" ftype="fastqsolexa" />
<param name="quality" value="33"/>
<param name="percent" value="100"/>
<output name="output" file="fastq_qual_filter1a.out" />
</test>
<test>
<!-- Test2: 80% of bases with quality 20 or higher -->
<param name="input" value="fastq_qual_filter1.fastq" />
<param name="input" value="fastq_qual_filter1.fastq" ftype="fastqsolexa"/>
<param name="quality" value="20"/>
<param name="percent" value="80"/>
<output name="output" file="fastq_qual_filter1b.out" />
tools/fastx_toolkit/fastq_to_fasta.xml
+8 -4
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@@ -1,10 +1,14 @@
<tool id="cshl_fastq_to_fasta" name="FASTQ to FASTA">
<description>converter</description>
<requirements><requirement type="package">fastx_toolkit</requirement></requirements>
<command>gunzip -cf $input | fastq_to_fasta $SKIPN $RENAMESEQ -o $output -v </command>
<command>gunzip -cf $input | fastq_to_fasta $SKIPN $RENAMESEQ -o $output -v
#if $input.ext == "fastqsanger":
-Q 33
#end if
</command>
<inputs>
<param format="fastq" name="input" type="data" label="FASTQ Library to convert" />
<param format="fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="FASTQ Library to convert" />
<param name="SKIPN" type="select" label="Discard sequences with unknown (N) bases ">
<option value="">yes</option>
@@ -21,14 +25,14 @@
<tests>
<test>
<!-- FASTQ-To-FASTA, keep N, don't rename -->
<param name="input" value="fastq_to_fasta1.fastq" />
<param name="input" value="fastq_to_fasta1.fastq" ftype="fastqsolexa" />
<param name="SKIPN" value=""/>
<param name="RENAMESEQ" value=""/>
<output name="output" file="fastq_to_fasta1a.out" />
</test>
<test>
<!-- FASTQ-To-FASTA, discard N, rename -->
<param name="input" value="fastq_to_fasta1.fastq" />
<param name="input" value="fastq_to_fasta1.fastq" ftype="fastqsolexa" />
<param name="SKIPN" value="no"/>
<param name="RENAMESEQ" value="yes"/>
<output name="output" file="fastq_to_fasta1b.out" />
tools/fastx_toolkit/fastx_artifacts_filter.xml
+6 -2
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@@ -1,10 +1,14 @@
<tool id="cshl_fastx_artifacts_filter" name="Remove sequencing artifacts">
<description></description>
<requirements><requirement type="package">fastx_toolkit</requirement></requirements>
<command>zcat -f '$input' | fastx_artifacts_filter -v -o "$output"</command>
<command>zcat -f '$input' | fastx_artifacts_filter -v -o "$output"
#if $input.ext == "fastqsanger":
-Q 33
#end if
</command>
<inputs>
<param format="fasta,fastqsanger,fastqsolexa" name="input" type="data" label="Library to filter" />
<param format="fasta,fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="Library to filter" />
</inputs>
tools/fastx_toolkit/fastx_barcode_splitter.xml
+2 -2
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@@ -5,7 +5,7 @@
<inputs>
<param format="txt" name="BARCODE" type="data" label="Barcodes to use" />
<param format="fasta,fastqsolexa" name="input" type="data" label="Library to split" />
<param format="fasta,fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="Library to split" />
<param name="EOL" type="select" label="Barcodes found at">
<option value="--bol">Start of sequence (5' end)</option>
@@ -22,7 +22,7 @@
<test>
<!-- Split a FASTQ file -->
<param name="BARCODE" value="fastx_barcode_splitter1.txt" />
<param name="input" value="fastx_barcode_splitter1.fastq" />
<param name="input" value="fastx_barcode_splitter1.fastq" ftype="fastqsolexa" />
<param name="EOL" value="Start of sequence (5' end)" />
<param name="mismatches" value="2" />
<param name="partial" value="0" />
tools/fastx_toolkit/fastx_clipper.xml
+2 -2
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@@ -9,7 +9,7 @@
</command>
<inputs>
<param format="fasta,fastqsolexa,fastqsanger" name="input" type="data" label="Library to clip" />
<param format="fasta,fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="Library to clip" />
<param name="minlength" size="4" type="integer" value="15">
<label>Minimum sequence length (after clipping, sequences shorter than this length will be discarded)</label>
@@ -56,7 +56,7 @@
#functional test with param value starting with - fails.
<tests>
<test>
<param name="input" value="fastx_clipper1.fastq" />
<param name="input" value="fastx_clipper1.fastq" ftype="fastqsolexa"/>
<param name="maxmismatches" value="2" />
<param name="minlength" value="15" />
<param name="clip_source_list" value="user" />
tools/fastx_toolkit/fastx_collapser.xml
+6 -2
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@@ -1,10 +1,14 @@
<tool id="cshl_fastx_collapser" name="Collapse">
<description>sequences</description>
<requirements><requirement type="package">fastx_toolkit</requirement></requirements>
<command>zcat -f '$input' | fastx_collapser -v -o '$output' </command>
<command>zcat -f '$input' | fastx_collapser -v -o '$output'
#if $input.ext == "fastqsanger":
-Q 33
#end if
</command>
<inputs>
<param format="fastqsolexa,fasta" name="input" type="data" label="Library to collapse" />
<param format="fasta,fastqsanger,fastqsolexa" name="input" type="data" label="Library to collapse" />
</inputs>
<!-- The order of sequences in the test output differ between 32 bit and 64 bit machines.
tools/fastx_toolkit/fastx_renamer.xml
+5 -1
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@@ -1,7 +1,11 @@
<tool id="cshl_fastx_renamer" name="Rename sequences" version="0.0.11" >
<description></description>
<requirements><requirement type="package">fastx_toolkit</requirement></requirements>
<command>zcat -f $input | fastx_renamer -n $TYPE -o $output -v </command>
<command>zcat -f $input | fastx_renamer -n $TYPE -o $output -v
#if $input.ext == "fastqsanger":
-Q 33
#end if
</command>
<inputs>
<param format="fastqsolexa,fasta,fastqsanger" name="input" type="data" label="FASTQ/A Library to rename" />
tools/fastx_toolkit/fastx_reverse_complement.xml
+7 -3
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@@ -1,9 +1,13 @@
<tool id="cshl_fastx_reverse_complement" name="Reverse-Complement">
<description></description>
<requirements><requirement type="package">fastx_toolkit</requirement></requirements>
<command>zcat -f '$input' | fastx_reverse_complement -v -o $output</command>
<command>zcat -f '$input' | fastx_reverse_complement -v -o $output
#if $input.ext == "fastqsanger":
-Q 33
#end if
</command>
<inputs>
<param format="fasta,fastqsolexa" name="input" type="data" label="Library to reverse-complement" />
<param format="fasta,fastqsolexa,fastqsanger" name="input" type="data" label="Library to reverse-complement" />
</inputs>
<tests>
@@ -14,7 +18,7 @@
</test>
<test>
<!-- Reverse-complement a FASTQ file -->
<param name="input" value="fastx_rev_comp2.fastq" />
<param name="input" value="fastx_rev_comp2.fastq" ftype="fastqsolexa"/>
<output name="output" file="fastx_reverse_complement2.out" />
</test>
</tests>
tools/fastx_toolkit/fastx_trimmer.xml
+7 -3
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@@ -1,10 +1,14 @@
<tool id="cshl_fastx_trimmer" name="Trim sequences">
<description></description>
<requirements><requirement type="package">fastx_toolkit</requirement></requirements>
<command>zcat -f '$input' | fastx_trimmer -v -f $first -l $last -o $output</command>
<command>zcat -f '$input' | fastx_trimmer -v -f $first -l $last -o $output
#if $input.ext == "fastqsanger":
-Q 33
#end if
</command>
<inputs>
<param format="fasta,fastqsanger" name="input" type="data" label="Library to clip" />
<param format="fasta,fastqsolexa,fastqsanger" name="input" type="data" label="Library to clip" />
<param name="first" size="4" type="integer" value="1">
<label>First base to keep</label>
@@ -25,7 +29,7 @@
</test>
<test>
<!-- Trim a FASTQ file - remove last 9 bases (e.g. keep only miRNA length sequences) -->
<param name="input" value="fastx_trimmer2.fastq" />
<param name="input" value="fastx_trimmer2.fastq" ftype="fastqsolexa"/>
<param name="first" value="1"/>
<param name="last" value="27"/>
<output name="output" file="fastx_trimmer2.out" />