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More modifications to fastx toolkit: added fastqsanger to input format list and changed the ascii offset param to select.

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This commit is contained in:
Guruprasad Anada
2009-09-15 11:28:50 -04:00
parent c4b8764d6f
commit 3877665d26
4 changed files with 15 additions and 9 deletions
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tools/fastx_toolkit/fasta_nucleotide_changer.xml
+3 -3
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@@ -10,21 +10,21 @@
</param>
</inputs>
<!--
Functional tests with param value starting with - fail.
<tests>
<test>
<!-- DNA-to-RNA -->
<param name="input" value="fasta_nuc_changer1.fasta" />
<param name="mode" value="-r" />
<output name="output" file="fasta_nuc_change1.out" />
</test>
<test>
<!-- RNA-to-DNA -->
<param name="input" value="fasta_nuc_changer2.fasta" />
<param name="mode" value="-d" />
<output name="output" file="fasta_nuc_change2.out" />
</test>
</tests>
-->
<outputs>
<data format="input" name="output" metadata_source="input" />
tools/fastx_toolkit/fastq_quality_converter.xml
+6 -3
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@@ -2,15 +2,18 @@
<description>(ASCII-Numeric)</description>
<command>zcat -f $input | fastq_quality_converter $QUAL_FORMAT -o $output -Q $offset</command>
<inputs>
<param format="fastqsolexa" name="input" type="data" label="Library to convert" />
<param format="fastqsolexa,fastqsanger" name="input" type="data" label="Library to convert" />
<param name="QUAL_FORMAT" type="select" label="Desired output format">
<option value="-a">ASCII (letters) quality scores</option>
<option value="-n">Numeric quality scores</option>
</param>
<param name="offset" size="4" type="integer" value="33" label="FASTQ ASCII offset" />
</inputs>
<param name="offset" type="select" label="FASTQ ASCII offset">
<option value="33">33</option>
<option value="64">64</option>
</param>
</inputs>
<tests>
<test>
tools/fastx_toolkit/fastq_quality_filter.xml
+1 -1
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@@ -4,7 +4,7 @@
<command>zcat -f '$input' | fastq_quality_filter -q $quality -p $percent -v -o $output</command>
<inputs>
<param format="fastqsolexa" name="input" type="data" label="Library to filter" />
<param format="fastqsolexa,fastqsanger" name="input" type="data" label="Library to filter" />
<param name="quality" size="4" type="integer" value="20">
<label>Quality cut-off value</label>
tools/fastx_toolkit/fastx_quality_statistics.xml
+5 -2
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@@ -3,8 +3,11 @@
<command>zcat -f $input | fastx_quality_stats -o $output -Q $offset</command>
<inputs>
<param format="fasta,fastqsolexa" name="input" type="data" label="Library to analyse" />
<param name="offset" size="4" type="integer" value="33" label="FASTQ ASCII offset" />
<param format="fasta,fastqsolexa,fastqsanger" name="input" type="data" label="Library to analyse" />
<param name="offset" type="select" label="FASTQ ASCII offset">
<option value="33">33</option>
<option value="64">64</option>
</param>
</inputs>
<tests>