Mercurial > repos > drosofff > annotation_collector

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planemo upload for repository https://bitbucket.org/drosofff/gedtools/
author drosofff
date Mon, 29 Jun 2015 03:39:57 -0400
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800bbe50ad70 planemo upload for repository https://bitbucket.org/drosofff/gedtools/
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1 <tool id="annotation_collector" name="Collect Annotation counts" version="0.9.0">
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2 <description> from matched fasta files</description>
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3 <command interpreter="python">
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4 annotation_collector.py
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5 $out_file
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6 $input1 $label1
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7 #for $q in $queries
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8 ${q.input2} ${q.label2}
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9 #end for
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10 $title
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11 </command>
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12 <inputs>
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13 <param label="Annotation Title" name="title" type="text" />
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14 <param label="fasta file to annotate" name="input1" type="data" format="fasta"/>
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15 <param label="category label" name="label1" type="text" />
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16 <repeat name="queries" title="Additional fasta file and label">
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17 <param label="Select" name="input2" type="data" format="fasta"/>
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18 <param label="Label" name="label2" type="text" />
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19 </repeat>
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20 </inputs>
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21 <outputs>
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22 <data format="tabular" label="Annotations" metadata_source="input1" name="out_file" />
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23 </outputs>
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24 <tests>
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25 <test>
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26 <param name="title" value="Test Title"/>
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27 <param name="input1" value="input1.fa" ftype="fasta"/>
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28 <param name="label1" value="label1" />
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29 <param name="queries_0|input2" value="input2.fa" ftype="fasta"/>
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30 <param name="queries_0|label2" value="label2" />
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31 <output name="out_file" file="output.tab" ftype="tabular" />
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32 </test>
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33 </tests>
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34 <help>
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35
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36 .. class:: warningmark
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37
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38 **WARNING:** Be careful not to agregate datasets of different kinds (e.g., datasets must be matched fasta files). This tool does not check if the datasets being annotated are in the same format.
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39
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40 -----
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41
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42 **What it does**
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43
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44 Generates Annotation Table from fasta files
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45
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46 Collect Annotation counts from matched fasta files.
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47 Counts number of lines in fasta files and outputs a
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48 tabular file with Label in the first column, number of fasta
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49 sequences in second column. Percent of counts is in the third
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50 column with the number of fasta entries in the first file
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51 set to 100%, and the remaining lines expressed as fractions.
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52
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53 </help>
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54 </tool>