| Next changeset 1:661b74ba4cc8 (2017-02-03) |
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Commit message:
Uploaded |
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added:
cluster-picker.xml |
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| diff -r 000000000000 -r 2040cda75d1f cluster-picker.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cluster-picker.xml Tue Jan 24 14:09:46 2017 -0500 |
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| @@ -0,0 +1,54 @@ +<tool id="cluster-pick" name="Cluster Picker" version="1.2.3"> + <description>cluster picker</description> +<requirements> + <requirement type="package" version="1.2.3">cluster-picker</requirement> +</requirements> +<!-- <command> <![CDATA[cluster-picker sequence_file tree_file init_threshold main_threshold dis_threshold size genetic_distance]]> </command> --> +<command> <![CDATA[cluster-picker]]> </command> +<inputs> + <param format="fasta" name="sequence_file" type="data" label="align" + help="Please enter fasta format sequences file name to process"/> + <param format="nwk" name="tree_file" type="data" label="tree" + help="Please enter newick format tree, with branch lengths and node support"/> + <param name="init_threshold" type="float" value="0.9" optional="true" + help="Please enter initial support threshold for these initial subtrees" label="initial threshold"> + </param> + <param name="main_threshold" type="float" value="0.9" optional="true" + help="Please enter main support threshold for clusters" label="main threshold"> + </param> + <param name="dis_threshold" type="float" value="0.045" optional="true" + help="Please enter genetic distance threshold for clusters in %" label="distance threshold"> + </param> + <param name="size" type="float" value="10" optional="true" + help="To output all cluster names for clusters of size >= X enter X" label="size"> + </param> + <param name="genetic_distance" type="select" label="genetic distance" + help="Please enter scoring type for genetic distance\n + abs = count absolute character differences\n + gap = disregard sites with -, ~, or n\n + valid = only count differences for sites with nucleotides: a, c, t, g in both sequences\n + ambiguity = disregard sites with -, ~, or n and do not count ambiguities as differences (e.g. a vs r is not a difference)"> + <option value="gap">gap</option> + <option value="abs">abs</option> + <option value="valid">valid</option> + <option value="ambiguity">ambiguity</option> + </param> +</inputs> +<outputs> + <data format="figTree"/> + <data format="nhx"/> + <data format="txt"/> + <data format="fasta"/> +</outputs> + +<tests> + <test> + <param name="input" value="fa_gc_content_input.fa"/> + <output name="out_file1" file="fa_gc_content_output.txt"/> + </test> +</tests> + +<help> +Cluster identification strategies differ between studies and as a consequence cluster definitions vary. +</help> +</tool> |