annotate presto_pairseq.xml @ 4:eed465eb14a3 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 1beb51cefbe9e6edc8930c7ae0421f28e7bb93c8
author iuc
date Fri, 04 Oct 2024 09:04:27 +0000
parents 49e7407445c3
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49e7407445c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit d52e3c9c53dd358e14e65a3a083e7d5c102f8697"
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1 <tool id="presto_pairseq" name="pRESTO PairSeq" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
0
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2 <description>Sorts and matches sequence records with matching coordinates across files</description>
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3 <macros>
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4 <import>presto_macros.xml</import>
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5 </macros>
4
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6 <expand macro="bio_tools"/>
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8 <expand macro="requirements"/>
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9
0
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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 $failed
0
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25 --outdir=.
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26 --outname=tmp
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27 ]]></command>
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28 <inputs>
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29 <param argument="-1" name="r1_in" type="data" format="fastq" label="Read 1 FASTQ/FASTA file."/>
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30 <param argument="-2" name="r2_in" type="data" format="fastq" label="Read 2 FASTQ/FASTA file."/>
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31 <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.">
f47efbc66fad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
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32 <expand macro="text-regex-validator"/>
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33 </param>
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34 <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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35 <expand macro="text-regex-validator"/>
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36 </param>
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37 <expand macro="presto-coord-param"/>
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38 <param argument="--failed" type="boolean" checked="false" truevalue="--failed" falsevalue="" label="Failed reads fastq output" />
0
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39 </inputs>
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40 <outputs>
4
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41 <data name="r1_out" format="fastq" from_work_dir="tmp-1_pair-pass.fastq" label="${tool.name} on ${on_string}: Paired R1"/>
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42 <data name="r2_out" format="fastq" from_work_dir="tmp-2_pair-pass.fastq" label="${tool.name} on ${on_string}: Paired R2"/>
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43 <!-- only give these 2 outputs if input failed_fastq=True-->
4
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44 <data name="r1_fail_out" format="fastq" from_work_dir="tmp-1_pair-fail.fastq" label="${tool.name} on ${on_string}: Unpaired R1">
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45 <filter>failed</filter>
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46 </data>
4
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47 <data name="r2_fail_out" format="fastq" from_work_dir="tmp-2_pair-fail.fastq" label="${tool.name} on ${on_string}: Unpaired R2">
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48 <filter>failed</filter>
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49 </data>
0
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50 </outputs>
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51 <tests>
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52 <test expect_num_outputs="2">
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53 <param name="r1_in" value="presto_pairseq_test1_r1_in.fastq"/>
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54 <param name="r2_in" value="presto_pairseq_test1_r2_in.fastq"/>
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55 <param name="r2_annotations" value="BARCODE"/>
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56 <param name="coord" value="illumina"/>
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57 <output name="r1_out" file="presto_pairseq_test1_r1_out.fastq" sort="true"/>
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58 <output name="r2_out" file="presto_pairseq_test1_r2_out.fastq" sort="true"/>
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59 </test>
3
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60 <test expect_num_outputs="4">
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61 <param name="r1_in" value="presto_pairseq_test1_r1_in.fastq"/>
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62 <param name="r2_in" value="presto_pairseq_test1_r2_in.fastq"/>
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63 <param name="r2_annotations" value="BARCODE"/>
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64 <param name="coord" value="illumina"/>
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65 <param name="failed" value="true"/>
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66 <output name="r1_out" file="presto_pairseq_test1_r1_out.fastq" sort="true"/>
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67 <output name="r2_out" file="presto_pairseq_test1_r2_out.fastq" sort="true"/>
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68 <output name="r1_fail_out">
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69 <assert_contents>
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70 <has_text text="@"/>
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71 </assert_contents>
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72 </output>
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73 <output name="r2_fail_out">
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74 <assert_contents>
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75 <has_text text="@"/>
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76 </assert_contents>
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77 </output>
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78 </test>
0
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79 </tests>
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80 <help><![CDATA[
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81 Sorts and matches sequence records with matching coordinates across files.
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82
1
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83 See the `pRESTO online help <@PRESTO_BASE_URL@/en/stable>`_ for more information.
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84
f47efbc66fad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
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85 @HELP_NOTE@
f47efbc66fad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
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86 ]]></help>
f47efbc66fad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
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87 <expand macro="citations" />
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88 </tool>