Mercurial > repos > mvdbeek > bam_readtagger

annotate normalize_readsizes.xml @ 76:8c3d8d38674a draft

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"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit fee3f43c26cd13ffdb81d64a3c7809c570ba2194"
author mvdbeek
date Mon, 23 Mar 2020 12:42:34 -0400
parents 2c7f70390b7c
children 6178c24ddd5a
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76
8c3d8d38674a "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit fee3f43c26cd13ffdb81d64a3c7809c570ba2194"
mvdbeek
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1 <tool id="normalize_readsizes" name="Normalize readsizes" version="0.5.23">
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2 <description>of multiple fastq files</description>
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3 <requirements>
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8c3d8d38674a "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit fee3f43c26cd13ffdb81d64a3c7809c570ba2194"
mvdbeek
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4 <requirement type="package" version="0.5.23">readtagger</requirement>
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5 </requirements>
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6 <version_command>normalize_readsizes --version</version_command>
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7 <command detect_errors="aggressive"><![CDATA[
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8 #for $i, $element in enumerate($input):
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9 ln -fs '$element' '${i}.${element.ext}' &&
f383ca1c5033 "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
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10 #end for
f383ca1c5033 "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
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11 normalize_readsizes
f383ca1c5033 "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
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12 #for $i, $element in enumerate($input):
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13 -i '${i}.${element.ext}'
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14 -o '${i}.out.${element.ext}'
f383ca1c5033 "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
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15 #end for
f383ca1c5033 "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
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16 #for $i, $element in enumerate($output):
f383ca1c5033 "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
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17 && mv '${i}.out.${element.ext}' '$element'
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18 #end for
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19 ]]></command>
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20 <inputs>
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21 <param name="input" type="data_collection" collection_type="list" label="Select collection of fastq datasets to normalize" format="fastqsanger,fastqsanger.gz"/>
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22 </inputs>
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23 <outputs>
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24 <collection name="output" type="list" structured_like="input" inherit_format="true"/>
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25 </outputs>
f383ca1c5033 "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
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26 <tests>
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27 <test>
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28 <param name="input">
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29 <collection type="list">
f383ca1c5033 "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
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30 <element name="a" value="long_reads_a.fastq" />
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31 <element name="b" value="long_reads_b.fastq" />
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32 </collection>
f383ca1c5033 "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
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33 </param>
f383ca1c5033 "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
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34 <param name="insert_reference" value="transposon"/>
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35 <output_collection name="output">
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36 <element name="a" value="long_reads_a_normalized.fastq" ftype="fastqsanger"/>
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37 <element name="b" value="long_reads_b_normalized.fastq" ftype="fastqsanger"/>
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38 </output_collection>
f383ca1c5033 "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
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39 </test>
f383ca1c5033 "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
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40 </tests>
f383ca1c5033 "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
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41 <help><![CDATA[
f383ca1c5033 "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
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42 Normalizes read size distributions across a collection of fastq files so that the read size distribution is the same
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43 across all datasets.
f383ca1c5033 "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
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44 ]]></help>
f383ca1c5033 "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
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45 </tool>