Mercurial > repos > iuc > trinity_contig_exn50_statistic

annotate contig_exn50_statistic.xml @ 2:a482a374577d draft

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author iuc
date Mon, 28 Aug 2017 16:54:37 -0400
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1 <tool id="trinity_contig_exn50_statistic" name="Compute contig Ex90N50 statistic and Ex90 transcript count" version="@WRAPPER_VERSION@.0">
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2 <description>from a Trinity assembly</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <command detect_errors="aggressive"><![CDATA[
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8 contig_ExN50_statistic.pl
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9 '$matrix'
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10 '$transcripts'
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11 > '$output'
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12 ]]></command>
1e8a2c87461a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit ed037d83415937b11a45a4611584e71e99ad1da0
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13 <inputs>
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14 <param format="tabular" name="matrix" type="data" label="Expression matrix" help="Matrix of normalized expression values produced by 'Build expression matrix for a de novo assembly of RNA-Seq data by Trinity' tool"/>
1e8a2c87461a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit ed037d83415937b11a45a4611584e71e99ad1da0
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15 <param format="fasta" name="transcripts" type="data" label="Transcripts" help="De novo assembly of RNA-Seq data"/>
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16 </inputs>
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17 <outputs>
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18 <data format="tabular" name="output" label="${tool.name} on ${on_string}: ExN50 statistics"/>
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19 </outputs>
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20 <tests>
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21 <test>
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22 <param name="matrix" value="count/contig_exn50_statistic/matrix.TMM.EXPR.matrix"/>
1e8a2c87461a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit ed037d83415937b11a45a4611584e71e99ad1da0
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23 <param name="transcripts" value="count/contig_exn50_statistic/Trinity.fasta"/>
1e8a2c87461a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit ed037d83415937b11a45a4611584e71e99ad1da0
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24 <output name="output" file="count/contig_exn50_statistic/ExN50.stats"/>
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25 </test>
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26 </tests>
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27 <help>
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28 <![CDATA[
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29 Trinity_ assembles transcript sequences from Illumina RNA-Seq data.
1e8a2c87461a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit ed037d83415937b11a45a4611584e71e99ad1da0
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30 This tool computes the N50 statistic limited to the top most highly expressed transcripts that represent x% of the total normalized expression data. This requires that you have first performed transcript abundance estimation with 'Align reads and estimate abundance for a de novo assembly of RNA-Seq data by Trinity' tool and that you have built the expression matrix with 'Build expression matrix for a de novo assembly of RNA-Seq data by Trinity' tool.
1e8a2c87461a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit ed037d83415937b11a45a4611584e71e99ad1da0
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32 **Inputs**
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34 It takes as input a transcriptome assembled with Trinity and the matrix of normalized expression values produced by 'Build expression matrix for a de novo assembly of RNA-Seq data by Trinity' tool.
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36 .. _Trinity: http://trinityrnaseq.github.io
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37 ]]>
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38 </help>
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39 <expand macro="citation" />
1e8a2c87461a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit ed037d83415937b11a45a4611584e71e99ad1da0
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40 </tool>