Mercurial > repos > rnateam > graphclust_preprocessing

comparison preprocessing.xml @ 6:e31c659be8bc draft

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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 6767a5ffb02052c844e9d862c79912f998f39d8e
author rnateam
date Mon, 20 Nov 2017 05:01:21 -0500
parents f4ad5dceb619
children 8634e06ae642
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5:f4ad5dceb619 6:e31c659be8bc
1 <tool id="preproc" name="Preprocessing" version="0.2"> 1 <tool id="preproc" name="Preprocessing" version="0.4">
2 <requirements> 2 <requirements>
3 <requirement type="package" version="0.1.12">graphclust-wrappers</requirement> 3 <requirement type="package" version="0.5.2">graphclust-wrappers</requirement>
4 <requirement type="package" version="3.0">zip</requirement>
5 <requirement type="package" version="1.70">biopython</requirement>
6
4 </requirements> 7 </requirements>
5 <stdio> 8 <stdio>
6 <exit_code range="1:" /> 9 <exit_code range="1:" />
7 </stdio> 10 </stdio>
8 <command> 11 <command>
15 18
16 #if $SHAPEdata: 19 #if $SHAPEdata:
17 && 20 &&
18 python '$__tool_directory__/splitSHAPE.py' 21 python '$__tool_directory__/splitSHAPE.py'
19 '$SHAPEdata' 22 '$SHAPEdata'
20 $max_length 23
21 #end if 24 #end if
25
26 #if $AlignmentData:
27 &&
28 python '$__tool_directory__/splitStockholm.py'
29 '$AlignmentData'
30
31 #end if
32
22 ]]> 33 ]]>
23 </command> 34 </command>
24 <inputs> 35 <inputs>
25 <param type="data" name="fastaFile" format="fasta" /> 36 <param type="data" name="fastaFile" format="fasta" />
26 <param type="data" name="SHAPEdata" format="txt" optional="true" label="SHAPE data"/> 37 <param type="data" name="SHAPEdata" format="txt" optional="true" label="SHAPE data"/>
38 <param type="data" name="AlignmentData" format="stockholm" optional="true" label="Alignments file"/>
27 <param name="max_length" type="integer" value="10000" size="5" label="window size"/> 39 <param name="max_length" type="integer" value="10000" size="5" label="window size"/>
28 <param name="in_winShift" type="integer" value="100" size="5" label="window shift in percent"/> 40 <param name="in_winShift" type="integer" value="100" size="5" label="window shift in percent"/>
29 <param name="min_seq_length" type="integer" value="5" size="5" label="minimum sequence length"/> 41 <param name="min_seq_length" type="integer" value="5" size="5" label="minimum sequence length"/>
30 </inputs> 42 </inputs>
31 <outputs> 43 <outputs>
32 <data name="data.fasta" format="fasta" from_work_dir="FASTA/data.fasta" label="data.fasta"/> 44 <data name="data.fasta" format="fasta" from_work_dir="FASTA/data.fasta" label="data.fasta"/>
33 <data name="data.map" format="txt" from_work_dir="FASTA/data.map" label="data.map"/> 45 <data name="data.map" format="txt" from_work_dir="FASTA/data.map" label="data.map"/>
34 <data name="data.names" format="txt" from_work_dir="FASTA/data.names" label="data.names"/> 46 <data name="data.names" format="txt" from_work_dir="FASTA/data.names" label="data.names"/>
35 <data name="data.fasta.scan" format="fasta" from_work_dir="FASTA/data.fasta.scan" label="data.fasta.scan"/> 47 <data name="data.fasta.scan" format="fasta" from_work_dir="FASTA/data.fasta.scan" label="data.fasta.scan"/>
36 <data name="FASTA" format="zip" from_work_dir="FASTA.zip" label="FASTA.ZIP"/> 48 <data name="FASTA" format="zip" from_work_dir="FASTA.zip" label="FASTA.ZIP"/>
37 <data name="shape_data_split" format="txt" from_work_dir="shape_data_split.react" label="SHAPE data splited"/> 49 <data name="shape_data_split" format="txt" from_work_dir="shape_data_split.react" label="SHAPE.data.split"/>
50 <data name="alignment_data_split" format="stockholm" from_work_dir="alignment_data_split.stk" label="alignments.data.stk"/>
38 </outputs> 51 </outputs>
39 <tests> 52 <tests>
40 <test> 53 <test>
41 <param name="fastaFile" value="input.fa"/> 54 <param name="fastaFile" value="input.fa"/>
42 <param name="max_length" value="10000"/> 55 <param name="max_length" value="10000"/>
53 <param name="SHAPEdata" value="sample_3.react"/> 66 <param name="SHAPEdata" value="sample_3.react"/>
54 <param name="max_length" value="100"/> 67 <param name="max_length" value="100"/>
55 <param name="in_winShift" value="50"/> 68 <param name="in_winShift" value="50"/>
56 <param name="min_seq_length" value="5"/> 69 <param name="min_seq_length" value="5"/>
57 <output name="shape_data_split" file="sample_3_shape_data_split.react" /> 70 <output name="shape_data_split" file="sample_3_shape_data_split.react" />
71 </test>
72 <test>
73 <param name="fastaFile" value="sample_4_representatives.fa"/>
74 <param name="AlignmentData" value="sample_4_all.stk"/>
75 <param name="max_length" value="50"/>
76 <param name="in_winShift" value="50"/>
77 <param name="min_seq_length" value="5"/>
78 <output name="alignment_data_split" file="sample_4_alignment_data_split.stk" />
58 </test> 79 </test>
59 </tests> 80 </tests>
60 <help> 81 <help>
61 <![CDATA[ 82 <![CDATA[
62 83