Mercurial > repos > iuc > slamdunk
diff alleyoop.xml @ 7:5a26589d95ad draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit b5aa6e762b55a9793dc7514efcda05eb2ccd529c"
| author | iuc |
|---|---|
| date | Sat, 25 Sep 2021 18:21:39 +0000 |
| parents | 141f65f7c7c8 |
| children |
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--- a/alleyoop.xml Tue Jul 13 14:01:12 2021 +0000 +++ b/alleyoop.xml Sat Sep 25 18:21:39 2021 +0000 @@ -1,9 +1,9 @@ -<tool id="alleyoop" name="Alleyoop" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> +<tool id="alleyoop" name="Alleyoop" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>- post-processing and QC of Slamdunk analyses</description> <macros> <import>macros.xml</import> </macros> - <expand macro="requirements" /> + <expand macro="requirements"/> <version_command>alleyoop --version</version_command> <command detect_errors="exit_code"><![CDATA[ #import re @@ -49,11 +49,11 @@ alleyoop rates -o ./stats -r reference.fa -mq $mq ./filter/*bam && -alleyoop utrrates -o ./stats -r reference.fa -b $Reference -t \${GALAXY_SLOTS:-1} -l $l -mq $mq ./filter/*bam && +alleyoop utrrates -o ./stats -r reference.fa -b $reference -t \${GALAXY_SLOTS:-1} -l $l -mq $mq ./filter/*bam && alleyoop tcperreadpos -o ./stats -r reference.fa -s ./snp -t \${GALAXY_SLOTS:-1} -l $l -mq $mq ./filter/*bam && -alleyoop tcperutrpos -o ./stats -r reference.fa -s ./snp -t \${GALAXY_SLOTS:-1} -l $l -b $Reference -mq $mq ./filter/*bam +alleyoop tcperutrpos -o ./stats -r reference.fa -s ./snp -t \${GALAXY_SLOTS:-1} -l $l -b $reference -mq $mq ./filter/*bam #if $bams: && alleyoop read-separator -o ./splitbams -s ./snp -r reference.fa ./filter/*bam @@ -61,62 +61,62 @@ ]]></command> <inputs> - <expand macro="reference_files" /> - <param name="reads" type="data" format="sam,bam" multiple="True" label="Slamdunk BAM files" /> - <param name="count_tsvs" type="data" format="tabular" multiple="True" label="Slamdunk Count TSV files" /> - <param name="variants" type="data" format="vcf" multiple="True" label="Slamdunk VCF files" /> - <param argument="-mq" type="integer" label="Minimum base quality" + <expand macro="reference_files"/> + <param name="reads" type="data" format="sam,bam" multiple="True" label="Slamdunk BAM files"/> + <param name="count_tsvs" type="data" format="tabular" multiple="True" label="Slamdunk Count TSV files"/> + <param name="variants" type="data" format="vcf" multiple="True" label="Slamdunk VCF files"/> + <param name="mq" argument="--min-basequality" type="integer" label="Minimum base quality" value="27" min="0" - help="Minimum base quality for T>C conversions (default: 27)." /> - <param argument="-l" type="integer" label="Read length" - value="50" min="50" help="Maximum read length (before trimming)." /> + help="Minimum base quality for T>C conversions (default: 27)."/> + <param name="l" argument="--max-read-length" type="integer" label="Read length" + value="50" min="50" help="Maximum read length (before trimming)."/> <param name="bams" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output T>C separated BAM files?" help="If this option is set to Yes, the Alleyoop read-separator module will be run to output BAM files of separated T>C reads from non T>C reads. Default: No"/> </inputs> <outputs> <collection name="outputSummary" type="list" label="${tool.name} on ${on_string}: Summary tables"> - <discover_datasets pattern="(?P<name>.+)\.txt$" format="tabular" directory="." visible="false" /> + <discover_datasets pattern="(?P<name>.+)\.txt$" format="tabular" directory="." visible="false"/> </collection> <collection name="outputStats" type="list" label="${tool.name} on ${on_string}: Stats tables"> - <discover_datasets pattern="(?P<name>.+)\.csv$" format="tabular" directory="./stats" visible="false" /> + <discover_datasets pattern="(?P<name>.+)\.csv$" format="tabular" directory="./stats" visible="false"/> </collection> <collection name="outputTCReads" type="list" label="${tool.name} on ${on_string}: TC Reads"> - <discover_datasets pattern="(?P<name>.+)_TCReads.bam$" format="bam" directory="./splitbams" visible="false" /> + <discover_datasets pattern="(?P<name>.+)_TCReads.bam$" format="bam" directory="./splitbams" visible="false"/> <filter>bams</filter> </collection> <collection name="outputbkgdReads" type="list" label="${tool.name} on ${on_string}: Background Reads"> - <discover_datasets pattern="(?P<name>.+)_backgroundReads.bam$" format="bam" directory="./splitbams" visible="false" /> + <discover_datasets pattern="(?P<name>.+)_backgroundReads.bam$" format="bam" directory="./splitbams" visible="false"/> <filter>bams</filter> </collection> </outputs> <tests> <!-- Ensure default output works --> <test expect_num_outputs="2"> - <param name="reference_source_selector" value="history" /> - <param name="ref_file" ftype="fasta" value="ref.fa" /> - <param name="Reference" ftype="bed" value="actb.bed" /> - <param name="reads" ftype="bam" value="reads1.bam,reads2.bam" /> - <param name="count_tsvs" ftype="tabular" value="reads1_tcount.tsv,reads2_tcount.tsv" /> - <param name="variants" ftype="vcf" value="reads1_snp.vcf,reads2_snp.vcf" /> - <param name="l" value="100" /> - <param name="mq" value="27" /> + <param name="reference_source_selector" value="history"/> + <param name="ref_file" ftype="fasta" value="ref.fa"/> + <param name="reference" ftype="bed" value="actb.bed"/> + <param name="reads" ftype="bam" value="reads1.bam,reads2.bam"/> + <param name="count_tsvs" ftype="tabular" value="reads1_tcount.tsv,reads2_tcount.tsv"/> + <param name="variants" ftype="vcf" value="reads1_snp.vcf,reads2_snp.vcf"/> + <param name="l" value="100"/> + <param name="mq" value="27"/> <output_collection name="outputSummary" count="2"> - <element name="summary" ftype="tabular" file="summary.txt" /> + <element name="summary" ftype="tabular" file="summary.txt" lines_diff="2"/> </output_collection> <output_collection name="outputStats" count="8"> - <element name="reads1_overallrates" ftype="tabular" file="reads1_overallrates.csv" /> + <element name="reads1_overallrates" ftype="tabular" file="reads1_overallrates.csv" lines_diff="2"/> </output_collection> </test> <!-- Ensure BAM output works --> <test expect_num_outputs="4"> - <param name="reference_source_selector" value="history" /> - <param name="ref_file" ftype="fasta" value="ref.fa" /> - <param name="Reference" ftype="bed" value="actb.bed" /> - <param name="reads" ftype="bam" value="reads1.bam,reads2.bam" /> - <param name="count_tsvs" ftype="tabular" value="reads1_tcount.tsv,reads2_tcount.tsv" /> - <param name="variants" ftype="vcf" value="reads1_snp.vcf,reads2_snp.vcf" /> - <param name="l" value="100" /> - <param name="mq" value="27" /> - <param name="bams" value="True" /> + <param name="reference_source_selector" value="history"/> + <param name="ref_file" ftype="fasta" value="ref.fa"/> + <param name="reference" ftype="bed" value="actb.bed"/> + <param name="reads" ftype="bam" value="reads1.bam,reads2.bam"/> + <param name="count_tsvs" ftype="tabular" value="reads1_tcount.tsv,reads2_tcount.tsv"/> + <param name="variants" ftype="vcf" value="reads1_snp.vcf,reads2_snp.vcf"/> + <param name="l" value="100"/> + <param name="mq" value="27"/> + <param name="bams" value="True"/> <output_collection name="outputTCReads" count="2"> <element name="reads1" ftype="bam" file="reads1_TCReads.bam" lines_diff="8"/> </output_collection> @@ -163,6 +163,6 @@ ]]></help> <citations> - <expand macro="citations" /> + <expand macro="citations"/> </citations> </tool>