Mercurial > repos > rnateam > graphclust_prepocessing_for_mlocarna
diff preMlocarna.xml @ 0:8ad3e79255c1 draft
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 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/preMlocarna.xml Fri Dec 16 07:36:24 2016 -0500 @@ -0,0 +1,82 @@ +<tool id="preMloc" name="premlocarna" version="0.1.0" > + <requirements> + <requirement type="package" version="0.1">graphclust-wrappers</requirement> + <requirement type="package" version='0.1'>pgma-simple</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + </stdio> + <command> + <![CDATA[ + + 'newpreMlocarna.pl' $CI '$fast_cluster' '$fasta_data' '$fast_cluster_sim' '$data_map' $knn '' + +]]> + </command> + <inputs> + <param type="data" name="fast_cluster" label="fast_cluster" format="txt" help="stokholm format" /> + <param type="data" name="fasta_data" label="fasta_data" format="fasta" help="fasta format" /> + <param type="data" name="fast_cluster_sim" label="fast_cluster_sim" format="txt" help="similarity sclores" /> + <param type="data" name="data_map" label="data_map" format="txt" help="data map" /> + <param name="CI" type="integer" value="1" size="5" label="Number of current iteration "/> + <param name="knn" type="integer" value="20" size="5" label="Number of nearest neighbors" help="must be the same as for previous step"/> + </inputs> + <outputs> + <collection name="centers" type="list" label="centers"> + <discover_datasets pattern="(?P<name>^[0-9]*\.[0-9]*\.center.fa$)" ext="txt" directory="CLUSTER" /> + </collection> + <collection name="trees" type="list" label="trees"> + <discover_datasets pattern="(?P<name>^[0-9]*\.[0-9]*\.tree$)" ext="txt" directory="CLUSTER" /> + </collection> + <collection name="cmFa" type="list" label="cmfinder_fa" > + <discover_datasets pattern="(?P<name>^[0-9]*\.[0-9]*\.cmfinder.fa$)" ext="txt" directory="CLUSTER" /> + </collection> + <collection name="model_tree_fa" type="list" label="model_tree_fa" > + <discover_datasets pattern="(?P<name>^[0-9]*\.[0-9]*\.model.tree.fa$)" ext="txt" directory="CLUSTER" /> + </collection> + <collection name="tree_matrix" type="list" label="tree_matrix" > + <discover_datasets pattern="(?P<name>^[0-9]*\.[0-9]*\.matrix.tree$)" ext="txt" directory="CLUSTER" /> + </collection> + </outputs> + <tests> + <test> + <param name="fast_cluster" value="data.svector.1.fast_cluster"/> + <param name="fasta_data" value="data.fasta"/> + <param name="fast_cluster_sim" value="data.svector.1.fast_cluster_sim"/> + <param name="data_map" value="data.map"/> + <param name="knn" value="20"/> + <param name="CI" value="1"/> + <output_collection name="centers"> + <element name="1.1.center.fa" file="CLUSTER/1.1.center.fa"/> + <element name="1.1.center.fa" file="CLUSTER/1.2.center.fa"/> + </output_collection> + <output_collection name="trees" > + <element name="1.1.tree" file="CLUSTER/1.1.tree"/> + <element name="1.2.tree" file="CLUSTER/1.2.tree"/> + </output_collection> + <output_collection name="cmFa"> + <element name="1.1.cmfinder.fa" file="CLUSTER/1.1.cmfinder.fa"/> + <element name="1.2.cmfinder.fa" file="CLUSTER/1.2.cmfinder.fa"/> + </output_collection> + <output_collection name="tree_matrix"> + <element name="1.1.matrix.tree" file="CLUSTER/1.1.matrix.tree"/> + <element name="1.2.matrix.tree" file="CLUSTER/1.2.matrix.tree"/> + </output_collection> + </test> + </tests> + <help> + <![CDATA[ + +**What it does** + +This tool prepares files for locarna step. + +.. class:: warningmark + +The number of nearest neighbors must be the same as in the previous step (NSPDK step) + +]]> + </help> + <citations> + </citations> +</tool>