Mercurial > repos > iuc > presto_alignsets

annotate presto_alignsets.xml @ 4:b401018e0614 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 1beb51cefbe9e6edc8930c7ae0421f28e7bb93c8
author iuc
date Fri, 04 Oct 2024 09:02:05 +0000
parents 0b4bd722367d
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0b4bd722367d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit d52e3c9c53dd358e14e65a3a083e7d5c102f8697"
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1 <tool id="presto_alignsets" name="pRESTO AlignSets" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>Multiple-align sequences with the same barcodes.</description>
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3 <macros>
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4 <import>presto_macros.xml</import>
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5 </macros>
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6 <expand macro="bio_tools"/>
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8 <expand macro="requirements"/>
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10 <version_command>AlignSets.py --version</version_command>
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11 <command detect_errors="exit_code"><![CDATA[
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12 ln -s '$fastq_in' in.fastq &&
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13 AlignSets.py muscle
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14 --nproc "\${GALAXY_SLOTS:-1}"
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15 -s in.fastq
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16 --bf '$bf'
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17 $div
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18 --outname=tmp
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19 #if $capture_log
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20 --log '$log_out'
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21 #end if
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22 ]]></command>
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24 <inputs>
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25 <param argument="-s" name="fastq_in" type="data" format="fastq" label="Input FASTQ file" help="FASTQ file of sequences with barcodes/UMIs in an annotation."/>
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26 <param argument="--bf" type="text" value="BARCODE" label="Barcode Field" help="Name of the annotation field which contains the barcode/UMI sequence."/>
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27 <param argument="--div" type="boolean" value="false" truevalue="--div" falsevalue="" label="Calculate Nucleotide Diversity" help="Specify to calculate nucleotide diversity of each set."/>
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28 <expand macro="presto-log-param"/>
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29 </inputs>
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31 <outputs>
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32 <data name="fastq_out" format="fastq" from_work_dir="tmp_align-pass.fastq"/>
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33 <expand macro="presto-log-output"/>
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34 </outputs>
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36 <tests>
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37 <test expect_num_outputs="2">
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38 <param name="fastq_in" value="presto_alignsets_test_in.fastq"/>
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39 <param name="capture_log" value="true"/>
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40 <output name="fastq_out" file="presto_alignsets_test_out.fastq" compare="sim_size" delta="15"/>
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41 <output name="log_out">
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42 <assert_contents>
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43 <has_text text="SEQCOUNT"/>
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44 </assert_contents>
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45 </output>
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46 </test>
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47 </tests>
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49 <help><![CDATA[
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50 Multiple aligns sequences with the same barcode to correct for any misalignments due to either different primer usage or insertions/deletions in the sequences.
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52 Only supports the "muscle" sub-command of pRESTO's AlignSets.py.
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53
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54 See the `pRESTO online help <@PRESTO_BASE_URL@/en/stable>`_ for more information.
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56 @HELP_NOTE@
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57 ]]></help>
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58 <expand macro="citations" />
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59 </tool>