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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
author dave
date Wed, 27 Nov 2019 15:24:18 +0000
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e48c040956ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
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1 <tool id="lofreq_viterbi" name="Realign reads" version="@WRAPPER_VERSION@0" python_template_version="3.5">
e48c040956ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
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2 <description>with LoFreq viterbi</description>
e48c040956ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
e48c040956ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
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6 <expand macro="requirements" />
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7 <command detect_errors="exit_code"><![CDATA[
e48c040956ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
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8 @PREPARE_REF@
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9 lofreq viterbi --ref '$reference_fasta_fn' --out - $keepflags --defqual $defqual '$reads' | samtools sort - -O BAM -o '$realigned'
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10 ]]></command>
e48c040956ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
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11 <inputs>
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12 <param name="reads" type="data" format="bam" label="Reads to realign" />
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13 <expand macro="reference_interface" />
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14 <param argument="--keepflags" type="boolean" truevalue="--keepflags" label="Don't delete flags MC, MD, NM, and A" help="These flags are all prone to changing during realignment" />
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15 <param argument="--defqual" type="integer" value="-1" label="Quality to assume for all bases with BQ2" />
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16 </inputs>
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17 <outputs>
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18 <data name="realigned" format="bam" label="${tool.name} on ${on_string}: Realigned reads" />
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19 </outputs>
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20 <tests>
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21 <test>
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22 <param name="reads" ftype="bam" value="lofreq-in1.bam" />
e48c040956ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
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23 <param name="ref_selector" value="history" />
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24 <param name="ref" ftype="fasta" value="pBR322.fa" />
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25 <output name="realigned" file="viterbi-out1.bam" />
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26 </test>
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27 <test>
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28 <param name="reads" ftype="bam" value="lofreq-in1.bam" />
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29 <param name="ref_selector" value="history" />
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30 <param name="keepflags" value="true" />
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31 <param name="ref" ftype="fasta" value="pBR322.fa" />
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32 <output name="realigned" file="viterbi-out2.bam" />
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33 </test>
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34 </tests>
e48c040956ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
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35 <help><![CDATA[
e48c040956ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
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36 Usage: lofreq viterbi [options] in.bam
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37
e48c040956ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit b8b08e76ebdca1fceef0da1b377eb4b6d45b0847-dirty"
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38 Options:
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39 -f | --ref FILE Indexed reference fasta file [null]
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40 -k | --keepflags Don't delete flags MC, MD, NM and A, which are all prone to change during realignment.
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41 -q | --defqual INT Assume INT as quality for all bases with BQ2. Default (=-1) is to use median quality of bases in read.
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42 -o | --out FILE Output BAM file [- = stdout = default]
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43 --verbose Be verbose
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44
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45 NOTE: Output BAM file will (likely) be unsorted (use samtools sort, e.g. lofreq viterbi ... | samtools sort -')
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46
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47 ]]></help>
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48 <expand macro="citations" />
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49 </tool>