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Corrected output labels to be in line with other tools for NGS tools: sam_to_bam, sam_merge, sam_pileup, bam_to_sam, PerM, bowtie_color_wrapper, bowtie_wrapper, bwa_wrapper, lastz_paired_reads_wrapper, lastz_wrapper, srma_wrapper

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This commit is contained in:
Kelly Vincent
2011-01-12 13:31:04 -05:00
parent 76b3cb5844
commit 8c13d8e6e8
11 changed files with 32 additions and 32 deletions
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tools/samtools/bam_to_sam.xml
+2 -2
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@@ -1,4 +1,4 @@
<tool id="bam_to_sam" name="BAM-to-SAM" version="1.0.0">
<tool id="bam_to_sam" name="BAM-to-SAM" version="1.0.1">
<requirements>
<requirement type="package">samtools</requirement>
</requirements>
@@ -12,7 +12,7 @@
<param name="input1" type="data" format="bam" label="BAM File to Convert" />
</inputs>
<outputs>
<data name="output1" format="sam" label="Converted SAM" />
<data format="sam" name="output1" label="${tool.name} on ${on_string}: converted SAM" />
</outputs>
<tests>
<test>
tools/samtools/sam_merge.xml
+2 -2
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@@ -1,4 +1,4 @@
<tool id="sam_merge" name="Merge BAM Files" version="1.1.0">
<tool id="sam_merge" name="Merge BAM Files" version="1.1.1">
<description>merges BAM files together</description>
<requirements>
<requirement type="package">samtools</requirement>
@@ -20,7 +20,7 @@
</repeat>
</inputs>
<outputs>
<data name="output1" format="bam" label="Merged BAM" />
<data format="bam" name="output1" label="${tool.name} on ${on_string}: merged BAM" />
</outputs>
<tests>
<!-- TODO: add ability to test framework to test without at least
tools/samtools/sam_pileup.xml
+2 -2
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@@ -1,4 +1,4 @@
<tool id="sam_pileup" name="Generate pileup" version="1.1.0">
<tool id="sam_pileup" name="Generate pileup" version="1.1.1">
<description>from BAM dataset</description>
<requirements>
<requirement type="package">samtools</requirement>
@@ -73,7 +73,7 @@
</conditional>
</inputs>
<outputs>
<data format="tabular" name="output1" label="Converted Pileup" />
<data format="tabular" name="output1" label="${tool.name} on ${on_string}: converted pileup" />
</outputs>
<tests>
<test>
tools/samtools/sam_to_bam.xml
+2 -2
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@@ -1,4 +1,4 @@
<tool id="sam_to_bam" name="SAM-to-BAM" version="1.1.0">
<tool id="sam_to_bam" name="SAM-to-BAM" version="1.1.1">
<description>converts SAM format to BAM format</description>
<requirements>
<requirement type="package">samtools</requirement>
@@ -34,7 +34,7 @@
</conditional>
</inputs>
<outputs>
<data name="output1" format="bam" label="Converted BAM" />
<data format="bam" name="output1" label="${tool.name} on ${on_string}: converted BAM" />
</outputs>
<tests>
<test>
tools/sr_mapping/PerM.xml
+4 -4
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@@ -1,4 +1,4 @@
<tool id="PerM" name="Map with PerM" version="1.1.1">
<tool id="PerM" name="Map with PerM" version="1.1.2">
<description>for SOLiD and Illumina</description>
<!-- works with PerM version 0.2.6 -->
<requirements>
@@ -159,11 +159,11 @@
</param>
</inputs>
<outputs>
<data name="output" format="sam" label="Mapped Reads" />
<data name="unmappedReadOut" format="fastqsanger" label="Unmapped Reads">
<data format="sam" name="output" label="${tool.name} on ${on_string}: mapped reads" />
<data format="fastqsanger" name="unmappedReadOut" label="${tool.name} on ${on_string}: unmapped reads">
<filter>bUnmappedRead == "true" and s["space"] == "base"</filter>
</data>
<data name="unmappedReadOutCS" format="fastqcssanger" label="Unmapped Reads">
<data format="fastqcssanger" name="unmappedReadOutCS" label="${tool.name} on ${on_string}: unmapped reads">
<filter>bUnmappedRead == "true" and s["space"] == "color"</filter>
</data>
</outputs>
tools/sr_mapping/bowtie_color_wrapper.xml
+6 -6
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@@ -1,4 +1,4 @@
<tool id="bowtie_color_wrapper" name="Map with Bowtie for SOLiD" version="1.1.0">
<tool id="bowtie_color_wrapper" name="Map with Bowtie for SOLiD" version="1.1.1">
<requirements><requirement type='package'>bowtie</requirement></requirements>
<description></description>
<command interpreter="python">
@@ -336,7 +336,7 @@
<param name="suppressHeader" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Suppress the header in the output SAM file" help="Bowtie produces SAM with several lines of header information by default" />
</inputs>
<outputs>
<data format="sam" name="output" label="Mapped Reads">
<data format="sam" name="output" label="${tool.name} on ${on_string}: mapped reads">
<actions>
<conditional name="refGenomeSource.genomeSource">
<when value="indexed">
@@ -350,7 +350,7 @@
</conditional>
</actions>
</data>
<data format="fastqcssanger" name="output_suppressed_reads_l" label="Suppressed Reads">
<data format="fastqcssanger" name="output_suppressed_reads_l" label="${tool.name} on ${on_string}: suppressed reads (L)">
<filter>((
singlePaired['sPaired'] == "single" and
singlePaired['sParams']['sSettingsType'] == "full" and
@@ -362,12 +362,12 @@
))
</filter>
</data>
<data format="fastqcssanger" name="output_suppressed_reads_r" label="Suppressed Reads (R)">
<data format="fastqcssanger" name="output_suppressed_reads_r" label="${tool.name} on ${on_string}: suppressed reads (R)">
<filter>singlePaired['sPaired'] == "paired"</filter>
<filter>singlePaired['pParams']['pSettingsType'] == "full"</filter>
<filter>singlePaired['pParams']['pMaxFile'] is True</filter>
</data>
<data format="fastqcssanger" name="output_unmapped_reads_l" label="Unmapped Reads (L)">
<data format="fastqcssanger" name="output_unmapped_reads_l" label="${tool.name} on ${on_string}: unmapped reads (L)">
<filter>
((
singlePaired['sPaired'] == "single" and
@@ -380,7 +380,7 @@
))
</filter>
</data>
<data format="fastqcssanger" name="output_unmapped_reads_r" label="Unmapped Reads (R)">
<data format="fastqcssanger" name="output_unmapped_reads_r" label="${tool.name} on ${on_string}: unmapped reads (R)">
<filter>singlePaired['sPaired'] == "paired"</filter>
<filter>singlePaired['pParams']['pSettingsType'] == "full"</filter>
<filter>singlePaired['pParams']['pUnmappedFile'] is True</filter>
tools/sr_mapping/bowtie_wrapper.xml
+6 -6
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@@ -1,4 +1,4 @@
<tool id="bowtie_wrapper" name="Map with Bowtie for Illumina" version="1.1.0">
<tool id="bowtie_wrapper" name="Map with Bowtie for Illumina" version="1.1.1">
<requirements><requirement type='package'>bowtie</requirement></requirements>
<description></description>
<parallelism method="basic"></parallelism>
@@ -319,7 +319,7 @@
<param name="suppressHeader" type="boolean" truevalue="true" falsevalue="false" checked="True" label="Suppress the header in the output SAM file" help="Bowtie produces SAM with several lines of header information by default" />
</inputs>
<outputs>
<data format="sam" name="output" label="Mapped Reads">
<data format="sam" name="output" label="${tool.name} on ${on_string}: mapped reads">
<actions>
<conditional name="refGenomeSource.genomeSource">
<when value="indexed">
@@ -333,7 +333,7 @@
</conditional>
</actions>
</data>
<data format="fastqsanger" name="output_suppressed_reads_l" label="Suppressed Reads">
<data format="fastqsanger" name="output_suppressed_reads_l" label="${tool.name} on ${on_string}: suppressed reads (L)">
<filter>((
singlePaired['sPaired'] == "single" and
singlePaired['sParams']['sSettingsType'] == "full" and
@@ -345,12 +345,12 @@
))
</filter>
</data>
<data format="fastqsanger" name="output_suppressed_reads_r" label="Suppressed Reads (R)">
<data format="fastqsanger" name="output_suppressed_reads_r" label="${tool.name} on ${on_string}: suppressed reads (R)">
<filter>singlePaired['sPaired'] == "paired"</filter>
<filter>singlePaired['pParams']['pSettingsType'] == "full"</filter>
<filter>singlePaired['pParams']['pMaxFile'] is True</filter>
</data>
<data format="fastqsanger" name="output_unmapped_reads_l" label="Unmapped Reads (L)">
<data format="fastqsanger" name="output_unmapped_reads_l" label="${tool.name} on ${on_string}: unmapped reads (L)">
<filter>
((
singlePaired['sPaired'] == "single" and
@@ -363,7 +363,7 @@
))
</filter>
</data>
<data format="fastqsanger" name="output_unmapped_reads_r" label="Unmapped Reads (R)">
<data format="fastqsanger" name="output_unmapped_reads_r" label="${tool.name} on ${on_string}: unmapped reads (R)">
<filter>singlePaired['sPaired'] == "paired"</filter>
<filter>singlePaired['pParams']['pSettingsType'] == "full"</filter>
<filter>singlePaired['pParams']['pUnmappedFile'] is True</filter>
tools/sr_mapping/bwa_wrapper.xml
+2 -2
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@@ -1,4 +1,4 @@
<tool id="bwa_wrapper" name="Map with BWA" version="1.2.0">
<tool id="bwa_wrapper" name="Map with BWA" version="1.2.1">
<description></description>
<parallelism method="basic"></parallelism>
<command interpreter="python">
@@ -113,7 +113,7 @@
<param name="suppressHeader" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Suppress the header in the output SAM file" help="BWA produces SAM with several lines of header information" />
</inputs>
<outputs>
<data format="sam" name="output" label="Mapped Reads">
<data format="sam" name="output" label="${tool.name} on ${on_string}: mapped reads">
<actions>
<conditional name="genomeSource.refGenomeSource">
<when value="indexed">
tools/sr_mapping/lastz_paired_reads_wrapper.xml
+2 -2
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@@ -1,4 +1,4 @@
<tool id="lastz_paired_reads_wrapper" name="Lastz paired reads" version="1.1.0">
<tool id="lastz_paired_reads_wrapper" name="Lastz paired reads" version="1.1.1">
<description> map short paired reads against reference sequence</description>
<command interpreter="python">lastz_paired_reads_wrapper.py
#if $seq_name.how_to_name=="yes":
@@ -47,7 +47,7 @@
</conditional>
</inputs>
<outputs>
<data format="sam" name="output1" label="Mapped Reads" />
<data format="sam" name="output1" label="${tool.name} on ${on_string}: mapped reads" />
</outputs>
<requirements>
<requirement type="package">lastz</requirement>
tools/sr_mapping/lastz_wrapper.xml
+2 -2
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@@ -1,4 +1,4 @@
<tool id="lastz_wrapper_2" name="Lastz" version="1.2.1">
<tool id="lastz_wrapper_2" name="Lastz" version="1.2.2">
<description> map short reads against reference sequence</description>
<command interpreter="python">lastz_wrapper.py
#if $seq_name.how_to_name=="yes":
@@ -129,7 +129,7 @@
</param>
</inputs>
<outputs>
<data format="tabular" name="output1" label="Mapped Reads">
<data format="tabular" name="output1" label="${tool.name} on ${on_string}: mapped reads">
<change_format>
<when input="out_format" value="sam" format="sam" />
</change_format>
tools/sr_mapping/srma_wrapper.xml
+2 -2
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@@ -1,4 +1,4 @@
<tool id="srma_wrapper" name="Re-align with SRMA" version="0.2.0">
<tool id="srma_wrapper" name="Re-align with SRMA" version="0.2.1">
<description></description>
<command interpreter="python">srma_wrapper.py
#if $refGenomeSource.refGenomeSource_type == "history":
@@ -61,7 +61,7 @@
</conditional>
</inputs>
<outputs>
<data format="bam" name="output" label="Re-aligned Reads">
<data format="bam" name="output" label="${tool.name} on ${on_string}: re-aligned reads">
<actions>
<conditional name="refGenomeSource.refGenomeSource_type">
<when value="built-in">