Mercurial > repos > iuc > multiqc

annotate fastp_plugin.xml @ 29:ef6bd40a30d2 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 4095773348da6faeb6096f58785b66898b09befa
author iuc
date Fri, 10 Oct 2025 20:11:35 +0000
parents 24002c7e6092
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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1 <macros>
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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2 <token name="@FASTP_COMMAND@"><![CDATA[
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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3 #set $pattern = "report_title"
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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4 #for $file in $repeat.software_cond.input
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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5 @ESCAPE_IDENTIFIER@
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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6 #set file_path = os.path.join($software_dir, str($identifier) + 'fastp.json')
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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7 ln -s '$file' '$file_path' &&
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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8 grep -q "$pattern" '$file_path' || die "'$pattern' or 'report_title' not found in the file" &&
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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9 #end for
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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10 ]]></token>
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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11 <xml name="fastp_form">
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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12 <param name="input" type="data" format="json" label="Output of fastp" help="It should be the json report from fastp containing 'report_title" multiple="true"/>
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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13 </xml>
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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14 <!-- add here your test files and tests, the more stringent the better -->
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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15 <xml name="fastp_test">
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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16 <test expect_num_outputs="3">
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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17 <repeat name="results">
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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18 <conditional name="software_cond">
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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19 <param name="software" value="fastp"/>
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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20 <param name="input" value="fastp1.json.txt,fastp2.json.txt"/>
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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21 </conditional>
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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22 </repeat>
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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23 <param name="title" value="Title of the report"/>
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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24 <param name="comment" value="Commment for the report"/>
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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25 <param name="flat" value="true"/>
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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26 <param name="export" value="true"/>
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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27 <output name="html_report">
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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28 <assert_contents>
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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29 <has_text text="Title of the report"/>
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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30 <has_text text="Commment for the report"/>
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
iuc
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31 <has_text text="All-in-one FASTQ preprocessor"/>
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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32 </assert_contents>
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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33 </output>
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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34 <output name="stats">
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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35 <assert_contents>
25
24002c7e6092 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 1805997f0c29291dd6fc96add4481422e28e6265
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36 <has_text text="fastp-pct_duplication"/>
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0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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37 <has_text text="R1_fq"/>
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24002c7e6092 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 1805997f0c29291dd6fc96add4481422e28e6265
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38 <has_text text="fastp-after_filtering_q30_rate"/>
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0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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39 <has_text text="bwa-mem-fastq1_fq"/>
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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40 <has_n_lines n="3"/>
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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41 <has_n_columns n="8"/>
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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42 </assert_contents>
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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43 </output>
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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44 <output_collection name="plots" type="list" count="15"/>
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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45 </test>
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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46 </xml>
0771dee34cff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
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47 </macros>