Mercurial > repos > iuc > lofreq_viterbi
diff lofreq_viterbi.xml @ 4:af7e416d8176 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 841c48994eb214a2f8718b1d1aca22bc38598528"
author | iuc |
---|---|
date | Mon, 15 Jun 2020 13:13:50 -0400 |
parents | ecd80c7c3886 |
children | aa35ee7f3ab2 |
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--- a/lofreq_viterbi.xml Fri May 29 15:24:28 2020 -0400 +++ b/lofreq_viterbi.xml Mon Jun 15 13:13:50 2020 -0400 @@ -1,28 +1,26 @@ -<tool id="lofreq_viterbi" name="Realign reads" version="@TOOL_VERSION@+galaxy1"> +<tool id="lofreq_viterbi" name="Realign reads" version="@TOOL_VERSION@+galaxy0"> <description>with LoFreq viterbi</description> <macros> <import>macros.xml</import> </macros> - <expand macro="requirements"> - <requirement type="package" version="1.9">samtools</requirement> - </expand> + <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @PREPARE_REF@ lofreq viterbi --ref '$reference_fasta_fn' - ${adv_options.delflags} + ${adv_options.keepflags} --defqual ${adv_options.bq2_handling.defqual} --out tmp.bam '$reads' && - samtools sort -T "\${TMPDIR:-.}" -@ \${GALAXY_SLOTS:-1} -O BAM -o '$realigned' tmp.bam + samtools sort --no-PG -T "\${TMPDIR:-.}" -@ \${GALAXY_SLOTS:-1} -O BAM -o '$realigned' tmp.bam ]]></command> <inputs> <param name="reads" type="data" format="bam" label="Reads to realign" /> <expand macro="reference_interface" /> <section name="adv_options" title="Advanced options" expanded="false"> - <param argument="--keepflags" name="delflags" type="boolean" truevalue="" falsevalue="--keepflags" checked="true" - label="Delete flags MC, MD, NM, and A?" - help="These flags are all prone to getting invalidated during realignment. Keep them only if you know what you are doing." /> + <param argument="--keepflags" type="boolean" truevalue="--keepflags" falsevalue="" checked="false" + label="Keep MC, MD, NM, and A flags?" + help="Re-alignment resets the MC, MD, NM, and A flags by default. The values of these tags depend on the exact alignment. Use this option only if you know what you are doing." /> <conditional name="bq2_handling"> <param name="replace_bq2" type="select" label="How to handle base qualities of 2?" @@ -51,17 +49,18 @@ <test> <param name="reads" ftype="bam" value="lofreq-in1.bam" /> <param name="ref_selector" value="history" /> + <param name="ref_selector" value="history" /> <param name="ref" ftype="fasta" value="pBR322.fa" /> - <output name="realigned" file="viterbi-out1.bam" /> + <output name="realigned" file="viterbi-out1.bam" ftype="bam" /> </test> <test> <param name="reads" ftype="bam" value="lofreq-in1.bam" /> <param name="ref_selector" value="history" /> <section name="adv_options"> - <param name="delflags" value="false" /> + <param name="keepflags" value="true" /> </section> <param name="ref" ftype="fasta" value="pBR322.fa" /> - <output name="realigned" file="viterbi-out2.bam" /> + <output name="realigned" file="viterbi-out2.bam" ftype="bam" /> </test> </tests> <help><![CDATA[