comparison SMART/galaxy/getReadDistribution.xml @ 6:769e306b7933

Change the repository level.
author yufei-luo
date Fri, 18 Jan 2013 04:54:14 -0500
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children 94ab73e8a190
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5:ea3082881bf8 6:769e306b7933
1 <tool id="getReadDistribution" name="get read distribution">
2 <description>Get Read Distribution v1.0.1: Plot the number of identical reads and give the most represented.</description>
3 <command interpreter="python">
4 ../Java/Python/WrappGetReadDistribution.py -i $formatType.inputFileName
5 #if $formatType.FormatInputFileName == 'fasta':
6 -f fasta
7 #elif $formatType.FormatInputFileName == 'fastq':
8 -f fastq
9 #end if
10
11 #if $optionnumber.number == 'Yes':
12 -n $optionnumber.bestNumber
13 #end if
14 #if $optionpercent.percent == 'Yes':
15 -p $optionpercent.percentage
16 #end if
17 -o $outputFile
18 </command>
19
20 <inputs>
21 <conditional name="formatType">
22 <param name="FormatInputFileName" type="select" label="Sequence input File Format ">
23 <option value="fasta">fasta</option>
24 <option value="fastq">fastq</option>
25 </param>
26 <when value="fasta">
27 <param name="inputFileName" format="fasta" type="data" label="Sequence input File"/>
28 </when>
29 <when value="fastq">
30 <param name="inputFileName" format="fastq" type="data" label="Sequence input File"/>
31 </when>
32 </conditional>
33
34 <conditional name="optionnumber">
35 <param name="number" type="select" label="keep the best n">
36 <option value="Yes">Yes</option>
37 <option value="No" selected="true">No</option>
38 </param>
39 <when value="Yes">
40 <param name="bestNumber" type="integer" value="0" />
41 </when>
42 <when value="No">
43 </when>
44 </conditional>
45
46 <conditional name="optionpercent">
47 <param name="percent" type="select" label="keep the best n percentage">
48 <option value="Yes">Yes</option>
49 <option value="No" selected="true">No</option>
50 </param>
51 <when value="Yes">
52 <param name="percentage" type="integer" value="0" />
53 </when>
54 <when value="No">
55 </when>
56 </conditional>
57
58 </inputs>
59
60 <outputs>
61 <data name="outputFile" format="tar" label="[getReadDistribution] tar out file" help="You can not see the results directly from galaxy, but you can download this tar output file."/>
62 </outputs>
63
64 <help>
65 This script gives a .tar out file, if you want to take look at the results, you have to download it.
66 </help>
67 </tool>