diff cluster-picker.xml @ 1:661b74ba4cc8 draft default tip

Uploaded

--- a/cluster-picker.xml	Tue Jan 24 14:09:46 2017 -0500
+++ b/cluster-picker.xml	Fri Feb 03 15:26:41 2017 -0500
@@ -3,12 +3,14 @@
 <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>
+<command> <![CDATA[ln -s '$sequence_file' seq.dat &&
+    ln -s '$tree_file' tree.dat &&
+    cluster-picker seq.dat tree.dat $init_threshold $main_threshold $dis_threshold $size $genetic_distance
+  ]]> </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"
+  <param format="nhx" 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">
@@ -19,13 +21,13 @@
   <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"
+  <param name="size" type="integer" 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
+          gap      	= disregard sites with -, ~, or n\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>
@@ -35,20 +37,37 @@
   </param>
 </inputs>
 <outputs>
-  <data format="figTree"/>
-  <data format="nhx"/>
-  <data format="txt"/>
-  <data format="fasta"/>
+  <data name='fig' format="figTree" from_work_dir="tree_clusterPicks.nwk.figTree"/>
+  <data name='tr' format="nhx" from_work_dir="tree_clusterPicks.nwk"/>
+  <data name='log' format="txt" from_work_dir="tree_clusterPicks_log.txt"/>
+  <data name='seq' format="fasta" from_work_dir="seq.dat_tree_clusterPicks.fasta"/>
 </outputs>
 
 <tests>
-  <test>
-    <param name="input" value="fa_gc_content_input.fa"/>
-    <output name="out_file1" file="fa_gc_content_output.txt"/>
-  </test>
+    <test>
+        <param name="sequence_file" value="dummy.fasta" />
+        <param name="tree_file" value="dummy.nhx" />
+        <param name="init_threshold" value="0.9" />
+        <param name="main_threshold" value="0.9" />
+        <param name="dis_threshold" value="0.045" />
+        <param name="size" value="10" />
+        <param name="genetic_distance" value="gap" />
+        <param name="main_threshold" file="0.9" />
+        <output name="fig" file="dummy.figTree" />
+    </test>
 </tests>
 
 <help>
 Cluster identification strategies differ between studies and as a consequence cluster definitions vary.
 </help>
+<citations>
+   <citation type="bibtex">@ARTICLE{cluster-picker,
+   author = {Ragonnet-Cronin, Manon, et al;},
+   title = {Automated analysis of phylogenetic clusters},
+   journal = {BMC bioinformatics},
+   year = {2013},
+   volume = {14.1},
+   pages = {317}}
+ </citation>
+</citations>
 </tool>