Mercurial > repos > mvdbeek > bam_readtagger
annotate normalize_readsizes.xml @ 80:c9361b7a025d draft
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit df2b1a906b8772810d995d7887e4e8f04aabc13a-dirty"
author | mvdbeek |
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date | Tue, 07 Apr 2020 15:25:30 -0400 |
parents | c42dd2551c9c |
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rev | line source |
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c42dd2551c9c
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit df2b1a906b8772810d995d7887e4e8f04aabc13a"
mvdbeek
parents:
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1 <tool id="normalize_readsizes" name="Normalize readsizes" version="0.5.25"> |
70
f383ca1c5033
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
mvdbeek
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2 <description>of multiple fastq files</description> |
f383ca1c5033
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
mvdbeek
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3 <requirements> |
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c42dd2551c9c
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit df2b1a906b8772810d995d7887e4e8f04aabc13a"
mvdbeek
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4 <requirement type="package" version="0.5.25">readtagger</requirement> |
70
f383ca1c5033
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
mvdbeek
parents:
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5 </requirements> |
f383ca1c5033
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
mvdbeek
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6 <version_command>normalize_readsizes --version</version_command> |
f383ca1c5033
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
mvdbeek
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7 <command detect_errors="aggressive"><![CDATA[ |
f383ca1c5033
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
mvdbeek
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8 #for $i, $element in enumerate($input): |
f383ca1c5033
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
mvdbeek
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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"
mvdbeek
parents:
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10 #end for |
f383ca1c5033
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
mvdbeek
parents:
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11 normalize_readsizes |
f383ca1c5033
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
mvdbeek
parents:
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12 #for $i, $element in enumerate($input): |
f383ca1c5033
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
mvdbeek
parents:
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13 -i '${i}.${element.ext}' |
f383ca1c5033
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
mvdbeek
parents:
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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"
mvdbeek
parents:
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15 #end for |
f383ca1c5033
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
mvdbeek
parents:
diff
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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"
mvdbeek
parents:
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17 && mv '${i}.out.${element.ext}' '$element' |
f383ca1c5033
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
mvdbeek
parents:
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18 #end for |
f383ca1c5033
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
mvdbeek
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19 ]]></command> |
f383ca1c5033
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
mvdbeek
parents:
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20 <inputs> |
f383ca1c5033
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
mvdbeek
parents:
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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"/> |
f383ca1c5033
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
mvdbeek
parents:
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22 </inputs> |
f383ca1c5033
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
mvdbeek
parents:
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23 <outputs> |
f383ca1c5033
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
mvdbeek
parents:
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24 <collection name="output" type="list" structured_like="input" inherit_format="true"/> |
f383ca1c5033
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
mvdbeek
parents:
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25 </outputs> |
f383ca1c5033
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
mvdbeek
parents:
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26 <tests> |
f383ca1c5033
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
mvdbeek
parents:
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27 <test> |
f383ca1c5033
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
mvdbeek
parents:
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28 <param name="input"> |
f383ca1c5033
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
mvdbeek
parents:
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29 <collection type="list"> |
f383ca1c5033
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
mvdbeek
parents:
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30 <element name="a" value="long_reads_a.fastq" /> |
f383ca1c5033
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
mvdbeek
parents:
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31 <element name="b" value="long_reads_b.fastq" /> |
f383ca1c5033
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
mvdbeek
parents:
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32 </collection> |
f383ca1c5033
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
mvdbeek
parents:
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33 </param> |
f383ca1c5033
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
mvdbeek
parents:
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34 <param name="insert_reference" value="transposon"/> |
f383ca1c5033
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
mvdbeek
parents:
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35 <output_collection name="output"> |
f383ca1c5033
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
mvdbeek
parents:
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36 <element name="a" value="long_reads_a_normalized.fastq" ftype="fastqsanger"/> |
f383ca1c5033
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
mvdbeek
parents:
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37 <element name="b" value="long_reads_b_normalized.fastq" ftype="fastqsanger"/> |
f383ca1c5033
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
mvdbeek
parents:
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38 </output_collection> |
f383ca1c5033
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
mvdbeek
parents:
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39 </test> |
f383ca1c5033
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
mvdbeek
parents:
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40 </tests> |
f383ca1c5033
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
mvdbeek
parents:
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41 <help><![CDATA[ |
f383ca1c5033
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
mvdbeek
parents:
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42 Normalizes read size distributions across a collection of fastq files so that the read size distribution is the same |
f383ca1c5033
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
mvdbeek
parents:
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43 across all datasets. |
f383ca1c5033
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
mvdbeek
parents:
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44 ]]></help> |
f383ca1c5033
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
mvdbeek
parents:
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45 </tool> |