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comparison lofreq_viterbi.xml @ 4:af7e416d8176 draft

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"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
comparison
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3:dbd9f2db9ed8 4:af7e416d8176
1 <tool id="lofreq_viterbi" name="Realign reads" version="@TOOL_VERSION@+galaxy1"> 1 <tool id="lofreq_viterbi" name="Realign reads" version="@TOOL_VERSION@+galaxy0">
2 <description>with LoFreq viterbi</description> 2 <description>with LoFreq viterbi</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"> 6 <expand macro="requirements" />
7 <requirement type="package" version="1.9">samtools</requirement>
8 </expand>
9 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
10 @PREPARE_REF@ 8 @PREPARE_REF@
11 lofreq viterbi 9 lofreq viterbi
12 --ref '$reference_fasta_fn' 10 --ref '$reference_fasta_fn'
13 ${adv_options.delflags} 11 ${adv_options.keepflags}
14 --defqual ${adv_options.bq2_handling.defqual} 12 --defqual ${adv_options.bq2_handling.defqual}
15 --out tmp.bam '$reads' && 13 --out tmp.bam '$reads' &&
16 14
17 samtools sort -T "\${TMPDIR:-.}" -@ \${GALAXY_SLOTS:-1} -O BAM -o '$realigned' tmp.bam 15 samtools sort --no-PG -T "\${TMPDIR:-.}" -@ \${GALAXY_SLOTS:-1} -O BAM -o '$realigned' tmp.bam
18 ]]></command> 16 ]]></command>
19 <inputs> 17 <inputs>
20 <param name="reads" type="data" format="bam" label="Reads to realign" /> 18 <param name="reads" type="data" format="bam" label="Reads to realign" />
21 <expand macro="reference_interface" /> 19 <expand macro="reference_interface" />
22 <section name="adv_options" title="Advanced options" expanded="false"> 20 <section name="adv_options" title="Advanced options" expanded="false">
23 <param argument="--keepflags" name="delflags" type="boolean" truevalue="" falsevalue="--keepflags" checked="true" 21 <param argument="--keepflags" type="boolean" truevalue="--keepflags" falsevalue="" checked="false"
24 label="Delete flags MC, MD, NM, and A?" 22 label="Keep MC, MD, NM, and A flags?"
25 help="These flags are all prone to getting invalidated during realignment. Keep them only if you know what you are doing." /> 23 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." />
26 <conditional name="bq2_handling"> 24 <conditional name="bq2_handling">
27 <param name="replace_bq2" type="select" 25 <param name="replace_bq2" type="select"
28 label="How to handle base qualities of 2?" 26 label="How to handle base qualities of 2?"
29 help="In sequenced reads obtained with Illumina sequencing pipelines before version 1.8, base quality 2 is special in that it serves as a general indicator of low quality of the corresponding bases. For such reads, the tool can make an optimistic guess of the real quality of such bases by replacing base qualities of 2 with the median of all other base qualities observed in the read. Alternatively, you can provide a fixed replacement value. For recently obtained sequencing data, just keep BQ2 values unchanged (the default) since they have no special meaning."> 27 help="In sequenced reads obtained with Illumina sequencing pipelines before version 1.8, base quality 2 is special in that it serves as a general indicator of low quality of the corresponding bases. For such reads, the tool can make an optimistic guess of the real quality of such bases by replacing base qualities of 2 with the median of all other base qualities observed in the read. Alternatively, you can provide a fixed replacement value. For recently obtained sequencing data, just keep BQ2 values unchanged (the default) since they have no special meaning.">
30 <option value="keep">Keep unchanged</option> 28 <option value="keep">Keep unchanged</option>
49 </outputs> 47 </outputs>
50 <tests> 48 <tests>
51 <test> 49 <test>
52 <param name="reads" ftype="bam" value="lofreq-in1.bam" /> 50 <param name="reads" ftype="bam" value="lofreq-in1.bam" />
53 <param name="ref_selector" value="history" /> 51 <param name="ref_selector" value="history" />
52 <param name="ref_selector" value="history" />
54 <param name="ref" ftype="fasta" value="pBR322.fa" /> 53 <param name="ref" ftype="fasta" value="pBR322.fa" />
55 <output name="realigned" file="viterbi-out1.bam" /> 54 <output name="realigned" file="viterbi-out1.bam" ftype="bam" />
56 </test> 55 </test>
57 <test> 56 <test>
58 <param name="reads" ftype="bam" value="lofreq-in1.bam" /> 57 <param name="reads" ftype="bam" value="lofreq-in1.bam" />
59 <param name="ref_selector" value="history" /> 58 <param name="ref_selector" value="history" />
60 <section name="adv_options"> 59 <section name="adv_options">
61 <param name="delflags" value="false" /> 60 <param name="keepflags" value="true" />
62 </section> 61 </section>
63 <param name="ref" ftype="fasta" value="pBR322.fa" /> 62 <param name="ref" ftype="fasta" value="pBR322.fa" />
64 <output name="realigned" file="viterbi-out2.bam" /> 63 <output name="realigned" file="viterbi-out2.bam" ftype="bam" />
65 </test> 64 </test>
66 </tests> 65 </tests>
67 <help><![CDATA[ 66 <help><![CDATA[
68 lofreq viterbi: Probabilistic realignment of mapped reads to correct mapping errors. 67 lofreq viterbi: Probabilistic realignment of mapped reads to correct mapping errors.
69 68