Mercurial > repos > iuc > ivar_removereads

annotate ivar_removereads.xml @ 3:3d18f8c3c0f6 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 47276c84cd0cd40084b7ccdf2e22c620ee1c10f6"
author iuc
date Fri, 05 Jun 2020 04:11:42 -0400
parents bd2a7d1316b9
children ee2beb764a7b
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bd2a7d1316b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
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1 <tool id="ivar_removereads" name="ivar removereads" version="@VERSION@+galaxy0">
bd2a7d1316b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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2 <description>Remove reads from trimmed BAM file</description>
bd2a7d1316b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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3 <macros>
bd2a7d1316b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
iuc
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4 <import>macros.xml</import>
bd2a7d1316b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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5 </macros>
bd2a7d1316b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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6 <expand macro="requirements" />
bd2a7d1316b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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7 <expand macro="version_command" />
bd2a7d1316b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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8 <command detect_errors="exit_code"><![CDATA[
bd2a7d1316b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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9 ln -s '$input_bam' sorted.bam &&
bd2a7d1316b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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10 ln -s '$primer_index' primers.txt &&
bd2a7d1316b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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11 ln -s '$input_bed' bed.bed &&
bd2a7d1316b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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12 ivar removereads
bd2a7d1316b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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13 -i sorted.bam
bd2a7d1316b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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14 -p removed_reads.bam
bd2a7d1316b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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15 -t primers.txt
bd2a7d1316b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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16 -b bed.bed
bd2a7d1316b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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17 ]]> </command>
bd2a7d1316b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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18 <inputs>
bd2a7d1316b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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19 <param name="input_bam" argument="-i" type="data" format="bam" label="Bam file" help="Aligned reads, to trim primers and quality"/>
bd2a7d1316b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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20 <param name="primer_index" argument="-t" type="data" format="txt" label="Text file with primer indices separated by spaces" help="This is the output of getmasked command"/>
bd2a7d1316b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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21 <param name="input_bed" argument="-b" type="data" format="bed" label="BED file with primer sequences and positions"/>
bd2a7d1316b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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22 </inputs>
bd2a7d1316b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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23 <outputs>
bd2a7d1316b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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24 <data name="output_bam" format="bam" label="${tool.name} on ${on_string}" from_work_dir="removed_reads.bam"/>
bd2a7d1316b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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25 </outputs>
bd2a7d1316b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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26 <tests>
bd2a7d1316b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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27 <test>
bd2a7d1316b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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28 <param name="input_bam" value="zika/Z52_a.trimmed.sorted.bam"/>
bd2a7d1316b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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29 <param name="primer_index" value="zika/primer_mismatchers_indices.txt"/>
bd2a7d1316b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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30 <param name="input_bed" value="zika/db/zika_primers.bed"/>
bd2a7d1316b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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31 <output name="output_bam" file="zika/Z52_a.masked.bam" compare="sim_size" delta="100000" />
bd2a7d1316b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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32 </test>
bd2a7d1316b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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33 </tests>
bd2a7d1316b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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34 <help><![CDATA[
bd2a7d1316b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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35 This command accepts an aligned and sorted BAM file trimmed using ivar trim
bd2a7d1316b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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36 and removes the reads corresponding to the supplied primer indices, which is
bd2a7d1316b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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37 the output of ivar getmasked command. Under the hood, ivar trim adds the
bd2a7d1316b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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38 zero based primer index (based on the BED file) to the BAM auxillary data for
bd2a7d1316b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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39 every read. Hence, ivar removereads will only work on BAM files that have
bd2a7d1316b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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40 been trimmed using ivar trim.
bd2a7d1316b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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41
bd2a7d1316b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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42 Documentation can be found at `<https://andersen-lab.github.io/ivar/html/manualpage.html>`_.
bd2a7d1316b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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43 ]]> </help>
bd2a7d1316b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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44 <expand macro="citations" />
bd2a7d1316b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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45 </tool>