Mercurial > repos > iuc > presto_pairseq

annotate presto_pairseq.xml @ 0:f47efbc66fad draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
author iuc
date Wed, 30 May 2018 15:37:15 -0400
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f47efbc66fad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
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1 <tool id="presto_pairseq" name="pRESTO PairSeq" version="@PRESTO_VERSION@">
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2 <description>Sorts and matches sequence records with matching coordinates across files</description>
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3
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4 <macros>
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5 <import>presto_macros.xml</import>
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6 </macros>
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7
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8 <expand macro="requirements"/>
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9
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10 <version_command>PairSeq.py --version</version_command>
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11 <command detect_errors="exit_code"><![CDATA[
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12 ln -s '$r1_in' r1.fastq &&
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13 ln -s '$r2_in' r2.fastq &&
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14 PairSeq.py
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15 -1 r1.fastq
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16 -2 r2.fastq
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17 --coord $coord
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18 #if $r1_annotations
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19 --1f $r1_annotations
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20 #end if
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21 #if $r2_annotations
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22 --2f $r2_annotations
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23 #end if
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24 --outdir=.
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25 --outname=tmp
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26 ]]></command>
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27 <inputs>
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28 <param argument="-1" name="r1_in" type="data" format="fastq" label="Read 1 FASTQ/FASTA file."/>
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29 <param argument="-2" name="r2_in" type="data" format="fastq" label="Read 2 FASTQ/FASTA file."/>
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30 <param argument="--1f" name="r1_annotations" type="text" optional="true" label="Annotation(s) to copy from R1 to R2." help="Multiple annotation must be space-separated.">
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31 <expand macro="text-regex-validator"/>
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32 </param>
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33 <param argument="--2f" name="r2_annotations" type="text" optional="true" label="Annotation(s) to copy from R2 to R1." help="Multiple annotation must be space-separated.">
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34 <expand macro="text-regex-validator"/>
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35 </param>
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36 <expand macro="presto-coord-param"/>
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37 </inputs>
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38 <outputs>
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39 <data name="r1_out" format="fastq" from_work_dir="tmp-1_pair-pass.fastq"/>
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40 <data name="r2_out" format="fastq" from_work_dir="tmp-2_pair-pass.fastq"/>
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41 </outputs>
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42
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43 <tests>
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44 <test>
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45 <param name="r1_in" value="presto_pairseq_test1_r1_in.fastq"/>
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46 <param name="r2_in" value="presto_pairseq_test1_r2_in.fastq"/>
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47 <param name="r2_annotations" value="BARCODE"/>
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48 <param name="coord" value="illumina"/>
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49 <output name="r1_out" file="presto_pairseq_test1_r1_out.fastq" sort="true"/>
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50 <output name="r2_out" file="presto_pairseq_test1_r2_out.fastq" sort="true"/>
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51 </test>
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52 </tests>
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53
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54 <help><![CDATA[
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55 Sorts and matches sequence records with matching coordinates across files.
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56
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57 See the `pRESTO online help <@PRESTO_URL_BASE@/PairSeq.html>`_ for more information.
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58
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59 @HELP_NOTE@
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60 ]]></help>
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61 <expand macro="citations" />
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62 </tool>