Mercurial > repos > rnateam > graphclust_prepocessing_for_mlocarna

comparison preMlocarna.xml @ 0:8ad3e79255c1 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/PrepareForMlocarna commit 21aaee40723b5341b4236edeb0e72995c2054053
author rnateam
date Fri, 16 Dec 2016 07:36:24 -0500
parents
children 8d3222b4b96b
comparison
equal deleted inserted replaced
-1:000000000000 0:8ad3e79255c1
1 <tool id="preMloc" name="premlocarna" version="0.1.0" >
2 <requirements>
3 <requirement type="package" version="0.1">graphclust-wrappers</requirement>
4 <requirement type="package" version='0.1'>pgma-simple</requirement>
5 </requirements>
6 <stdio>
7 <exit_code range="1:" />
8 </stdio>
9 <command>
10 <![CDATA[
11
12 'newpreMlocarna.pl' $CI '$fast_cluster' '$fasta_data' '$fast_cluster_sim' '$data_map' $knn ''
13
14 ]]>
15 </command>
16 <inputs>
17 <param type="data" name="fast_cluster" label="fast_cluster" format="txt" help="stokholm format" />
18 <param type="data" name="fasta_data" label="fasta_data" format="fasta" help="fasta format" />
19 <param type="data" name="fast_cluster_sim" label="fast_cluster_sim" format="txt" help="similarity sclores" />
20 <param type="data" name="data_map" label="data_map" format="txt" help="data map" />
21 <param name="CI" type="integer" value="1" size="5" label="Number of current iteration "/>
22 <param name="knn" type="integer" value="20" size="5" label="Number of nearest neighbors" help="must be the same as for previous step"/>
23 </inputs>
24 <outputs>
25 <collection name="centers" type="list" label="centers">
26 <discover_datasets pattern="(?P&lt;name&gt;^[0-9]*\.[0-9]*\.center.fa$)" ext="txt" directory="CLUSTER" />
27 </collection>
28 <collection name="trees" type="list" label="trees">
29 <discover_datasets pattern="(?P&lt;name&gt;^[0-9]*\.[0-9]*\.tree$)" ext="txt" directory="CLUSTER" />
30 </collection>
31 <collection name="cmFa" type="list" label="cmfinder_fa" >
32 <discover_datasets pattern="(?P&lt;name&gt;^[0-9]*\.[0-9]*\.cmfinder.fa$)" ext="txt" directory="CLUSTER" />
33 </collection>
34 <collection name="model_tree_fa" type="list" label="model_tree_fa" >
35 <discover_datasets pattern="(?P&lt;name&gt;^[0-9]*\.[0-9]*\.model.tree.fa$)" ext="txt" directory="CLUSTER" />
36 </collection>
37 <collection name="tree_matrix" type="list" label="tree_matrix" >
38 <discover_datasets pattern="(?P&lt;name&gt;^[0-9]*\.[0-9]*\.matrix.tree$)" ext="txt" directory="CLUSTER" />
39 </collection>
40 </outputs>
41 <tests>
42 <test>
43 <param name="fast_cluster" value="data.svector.1.fast_cluster"/>
44 <param name="fasta_data" value="data.fasta"/>
45 <param name="fast_cluster_sim" value="data.svector.1.fast_cluster_sim"/>
46 <param name="data_map" value="data.map"/>
47 <param name="knn" value="20"/>
48 <param name="CI" value="1"/>
49 <output_collection name="centers">
50 <element name="1.1.center.fa" file="CLUSTER/1.1.center.fa"/>
51 <element name="1.1.center.fa" file="CLUSTER/1.2.center.fa"/>
52 </output_collection>
53 <output_collection name="trees" >
54 <element name="1.1.tree" file="CLUSTER/1.1.tree"/>
55 <element name="1.2.tree" file="CLUSTER/1.2.tree"/>
56 </output_collection>
57 <output_collection name="cmFa">
58 <element name="1.1.cmfinder.fa" file="CLUSTER/1.1.cmfinder.fa"/>
59 <element name="1.2.cmfinder.fa" file="CLUSTER/1.2.cmfinder.fa"/>
60 </output_collection>
61 <output_collection name="tree_matrix">
62 <element name="1.1.matrix.tree" file="CLUSTER/1.1.matrix.tree"/>
63 <element name="1.2.matrix.tree" file="CLUSTER/1.2.matrix.tree"/>
64 </output_collection>
65 </test>
66 </tests>
67 <help>
68 <![CDATA[
69
70 **What it does**
71
72 This tool prepares files for locarna step.
73
74 .. class:: warningmark
75
76 The number of nearest neighbors must be the same as in the previous step (NSPDK step)
77
78 ]]>
79 </help>
80 <citations>
81 </citations>
82 </tool>