Mercurial > repos > mvdbeek > damid_deseq2_to_bedgraph

annotate damid_interpolate.xml @ 0:755cbe6825b5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
author mvdbeek
date Fri, 14 Dec 2018 06:27:41 -0500
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children 210b7f4c9acb
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755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
parents:
diff changeset
1 <tool id="damid_interpolate" name="Interpolate GATC signal" version="0.1.0">
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
parents:
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2 <description>from DESeq2 processed DamID data</description>
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
parents:
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3 <requirements>
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
parents:
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4 <requirement type="package" version="2.4.1">traces</requirement>
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
parents:
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5 <requirement type="package" version="7">click</requirement>
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
parents:
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6 <requirement type="package" version="0.23.4">pandas</requirement>
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
parents:
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7 </requirements>
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
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8 <command detect_errors="exit_code"><![CDATA[
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
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9 python '$__tool_directory__/damid_to_bedgraph.py' '$input' '$output' --resolution $resolution
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
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10 ]]></command>
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
parents:
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11 <inputs>
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
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12 <param name="input" type="data" format="tabular" label="Select DESeq2 result file for GATC sites"/>
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
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13 <param argument="--resolution" type="integer" value="50" label="Select resolution for intervals"/>
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
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14 </inputs>
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
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15 <outputs>
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
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16 <data name="output" format="bedgraph"/>
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
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17 </outputs>
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
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18 <tests>
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
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19 <test>
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
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20 <param name="input" value="test_data.tab"/>
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
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21 <output name="output" value="line_count_50.tab"/>
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
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22 </test>
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
parents:
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23 <test>
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
parents:
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24 <param name="input" value="test_data.tab"/>
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
parents:
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25 <param name="resolution" value="100"/>
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
parents:
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26 <output name="output" value="line_count_100.tab"/>
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
parents:
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27 </test>
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
parents:
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28 </tests>
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
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29 <help><![CDATA[
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
parents:
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30 Takes a deseq2 output file and generate a bedgraph file, where the score column
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
parents:
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31 is the log2 fold change value interpolated for intervals of the size selected in
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
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32 "Select resolution for intervals".
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
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33 ]]></help>
755cbe6825b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damid_deseq2_to_bedgraph commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
parents:
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34 </tool>