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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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1 <tool id="annotation_collector" name="Collect Annotation counts" version="0.9.0">
2 <description> from matched fasta files</description>
3 <command interpreter="python">
4 annotation_collector.py
5 $out_file
6 $input1 $label1
7 #for $q in $queries
8 ${q.input2} ${q.label2}
9 #end for
10 $title
11 </command>
12 <inputs>
13 <param label="Annotation Title" name="title" type="text" />
14 <param label="fasta file to annotate" name="input1" type="data" format="fasta"/>
15 <param label="category label" name="label1" type="text" />
16 <repeat name="queries" title="Additional fasta file and label">
17 <param label="Select" name="input2" type="data" format="fasta"/>
18 <param label="Label" name="label2" type="text" />
19 </repeat>
20 </inputs>
21 <outputs>
22 <data format="tabular" label="Annotations" metadata_source="input1" name="out_file" />
23 </outputs>
24 <tests>
25 <test>
26 <param name="title" value="Test Title"/>
27 <param name="input1" value="input1.fa" ftype="fasta"/>
28 <param name="label1" value="label1" />
29 <param name="queries_0|input2" value="input2.fa" ftype="fasta"/>
30 <param name="queries_0|label2" value="label2" />
31 <output name="out_file" file="output.tab" ftype="tabular" />
32 </test>
33 </tests>
34 <help>
35
36 .. class:: warningmark
37
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.
39
40 -----
41
42 **What it does**
43
44 Generates Annotation Table from fasta files
45
46 Collect Annotation counts from matched fasta files.
47 Counts number of lines in fasta files and outputs a
48 tabular file with Label in the first column, number of fasta
49 sequences in second column. Percent of counts is in the third
50 column with the number of fasta entries in the first file
51 set to 100%, and the remaining lines expressed as fractions.
52
53 </help>
54 </tool>