Mercurial > repos > iuc > multiqc

annotate sambamba_plugin.xml @ 28:31c42a2c02d3 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 7f250f4b9484eceef360ba62ef519c94b56c0b97
author iuc
date Wed, 19 Feb 2025 16:01:14 +0000
parents d2aaac19f42f
children
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26
d2aaac19f42f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 881c4f072b1c9bd2355ba41a58e2c04d43f5ac6b
iuc
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1 <macros>
d2aaac19f42f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 881c4f072b1c9bd2355ba41a58e2c04d43f5ac6b
iuc
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2 <token name="@SAMBAMBA_COMMAND@"><![CDATA[
d2aaac19f42f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 881c4f072b1c9bd2355ba41a58e2c04d43f5ac6b
iuc
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3 #set $pattern = "finding positions of the duplicate reads in the file"
d2aaac19f42f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 881c4f072b1c9bd2355ba41a58e2c04d43f5ac6b
iuc
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4 @LN_FILES@
d2aaac19f42f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 881c4f072b1c9bd2355ba41a58e2c04d43f5ac6b
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5 ]]></token>
d2aaac19f42f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 881c4f072b1c9bd2355ba41a58e2c04d43f5ac6b
iuc
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6 <xml name="sambamba_form">
d2aaac19f42f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 881c4f072b1c9bd2355ba41a58e2c04d43f5ac6b
iuc
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7 <param name="input" type="data" format="txt" multiple="true" label="Output of Sambamba markdup" help="It should contain 'finding positions of the duplicate reads in the file'"/>
d2aaac19f42f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 881c4f072b1c9bd2355ba41a58e2c04d43f5ac6b
iuc
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8 </xml>
d2aaac19f42f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 881c4f072b1c9bd2355ba41a58e2c04d43f5ac6b
iuc
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9 <xml name="sambamba_test">
d2aaac19f42f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 881c4f072b1c9bd2355ba41a58e2c04d43f5ac6b
iuc
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10 <test expect_num_outputs="3">
d2aaac19f42f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 881c4f072b1c9bd2355ba41a58e2c04d43f5ac6b
iuc
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11 <repeat name="results">
d2aaac19f42f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 881c4f072b1c9bd2355ba41a58e2c04d43f5ac6b
iuc
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12 <conditional name="software_cond">
d2aaac19f42f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 881c4f072b1c9bd2355ba41a58e2c04d43f5ac6b
iuc
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13 <param name="software" value="sambamba"/>
d2aaac19f42f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 881c4f072b1c9bd2355ba41a58e2c04d43f5ac6b
iuc
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14 <param name="input" value="sambamba.txt"/>
d2aaac19f42f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 881c4f072b1c9bd2355ba41a58e2c04d43f5ac6b
iuc
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15 </conditional>
d2aaac19f42f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 881c4f072b1c9bd2355ba41a58e2c04d43f5ac6b
iuc
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16 </repeat>
d2aaac19f42f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 881c4f072b1c9bd2355ba41a58e2c04d43f5ac6b
iuc
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17 <param name="title" value="Title of the report"/>
d2aaac19f42f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 881c4f072b1c9bd2355ba41a58e2c04d43f5ac6b
iuc
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18 <param name="comment" value="Commment for the report"/>
d2aaac19f42f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 881c4f072b1c9bd2355ba41a58e2c04d43f5ac6b
iuc
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19 <param name="flat" value="true"/>
d2aaac19f42f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 881c4f072b1c9bd2355ba41a58e2c04d43f5ac6b
iuc
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20 <param name="export" value="true"/>
d2aaac19f42f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 881c4f072b1c9bd2355ba41a58e2c04d43f5ac6b
iuc
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21 <output name="html_report">
d2aaac19f42f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 881c4f072b1c9bd2355ba41a58e2c04d43f5ac6b
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22 <assert_contents>
d2aaac19f42f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 881c4f072b1c9bd2355ba41a58e2c04d43f5ac6b
iuc
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23 <has_text text="Title of the report"/>
d2aaac19f42f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 881c4f072b1c9bd2355ba41a58e2c04d43f5ac6b
iuc
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24 <has_text text="Commment for the report"/>
d2aaac19f42f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 881c4f072b1c9bd2355ba41a58e2c04d43f5ac6b
iuc
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25 <has_text text="Sambamba Markdup"/>
d2aaac19f42f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 881c4f072b1c9bd2355ba41a58e2c04d43f5ac6b
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26 </assert_contents>
d2aaac19f42f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 881c4f072b1c9bd2355ba41a58e2c04d43f5ac6b
iuc
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27 </output>
d2aaac19f42f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 881c4f072b1c9bd2355ba41a58e2c04d43f5ac6b
iuc
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28 <output name="stats">
d2aaac19f42f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 881c4f072b1c9bd2355ba41a58e2c04d43f5ac6b
iuc
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29 <assert_contents>
d2aaac19f42f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 881c4f072b1c9bd2355ba41a58e2c04d43f5ac6b
iuc
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30 <has_text text="Sample"/>
d2aaac19f42f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 881c4f072b1c9bd2355ba41a58e2c04d43f5ac6b
iuc
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31 <has_text text="sambamba_markdup-duplicate_rate"/>
d2aaac19f42f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 881c4f072b1c9bd2355ba41a58e2c04d43f5ac6b
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32 <has_n_lines n="2"/>
d2aaac19f42f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 881c4f072b1c9bd2355ba41a58e2c04d43f5ac6b
iuc
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33 <has_n_columns n="2"/>
d2aaac19f42f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 881c4f072b1c9bd2355ba41a58e2c04d43f5ac6b
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34 </assert_contents>
d2aaac19f42f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 881c4f072b1c9bd2355ba41a58e2c04d43f5ac6b
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35 </output>
d2aaac19f42f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 881c4f072b1c9bd2355ba41a58e2c04d43f5ac6b
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36 <output_collection name="plots" type="list" count="0"/>
d2aaac19f42f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 881c4f072b1c9bd2355ba41a58e2c04d43f5ac6b
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37 </test>
d2aaac19f42f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 881c4f072b1c9bd2355ba41a58e2c04d43f5ac6b
iuc
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38 </xml>
d2aaac19f42f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 881c4f072b1c9bd2355ba41a58e2c04d43f5ac6b
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39 </macros>