# HG changeset patch
# User jasper
# Date 1486153601 18000
# Node ID 661b74ba4cc8a3b172c6e05682f1db274f683899
# Parent  2040cda75d1fb1744661eb7784a5dc89e8f5627b
Uploaded

diff -r 2040cda75d1f -r 661b74ba4cc8 cluster-picker.xml
--- 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>
diff -r 2040cda75d1f -r 661b74ba4cc8 test-data/._.DS_Store
Binary file test-data/._.DS_Store has changed
diff -r 2040cda75d1f -r 661b74ba4cc8 test-data/dummy.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dummy.fasta	Fri Feb 03 15:26:41 2017 -0500
@@ -0,0 +1,8 @@
+-e >seq1
+ATTA
+>seq2
+ATTA
+>seq3
+ATTA
+>seq4
+ATTA
diff -r 2040cda75d1f -r 661b74ba4cc8 test-data/dummy.figTree
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dummy.figTree	Fri Feb 03 15:26:41 2017 -0500
@@ -0,0 +1,1 @@
+#NEXUS
begin taxa;
dimensions ntax=4;
	taxlabels
	seq1
	seq2
	seq3
	seq4
	;
end;
begin trees;
	tree tree_1 = [&R] (((seq1:0.001,seq2:0.002)[&support=0.0]:0.001,seq3:0.005)[&support=0.0]:0.004,seq4:0.003)[&support=0.0]:0.001;
end;
begin figtree;
	set appearance.backgroundColorAttribute="User Selection";
	set appearance.backgroundColour=#-1;
	set appearance.branchColorAttribute="User Selection";
	set appearance.branchLineWidth=1.0;
	set appearance.foregroundColour=#-16777216;
	set appearance.selectionColour=#-2144520576;
	set branchLabels.colorAttribute="User Selection";
	set branchLabels.displayAttribute="Branch times";
	set branchLabels.fontName="sansserif";
	set branchLabels.fontSize=8;
	set branchLabels.fontStyle=0;
	set branchLabels.isShown=false;
	set branchLabels.significantDigits=4;
	set layout.expansion=0;
	set layout.layoutType="RECTILINEAR";
	set layout.zoom=0;
	set nodeBars.barWidth=4.0;
	set nodeLabels.colorAttribute="User Selection";
	set nodeLabels.displayAttribute="support";
	set nodeLabels.fontName="Arial";
	set nodeLabels.fontSize=10;
	set nodeLabels.fontStyle=0;
	set nodeLabels.isShown=true;
	set nodeLabels.significantDigits=3;
	set polarLayout.alignTipLabels=false;
	set polarLayout.angularRange=0;
	set polarLayout.rootAngle=0;
	set polarLayout.rootLength=100;
	set polarLayout.showRoot=true;
	set radialLayout.spread=0.0;
	set rectilinearLayout.alignTipLabels=false;
	set rectilinearLayout.curvature=0;
	set rectilinearLayout.rootLength=100;
	set scale.offsetAge=0.0;
	set scale.rootAge=1.0;
	set scale.scaleFactor=1.0;
	set scale.scaleRoot=false;
	set scaleAxis.automaticScale=true;
	set scaleAxis.fontSize=8.0;
	set scaleAxis.isShown=false;
	set scaleAxis.lineWidth=1.0;
	set scaleAxis.majorTicks=1.0;
	set scaleAxis.origin=0.0;
	set scaleAxis.reverseAxis=false;
	set scaleAxis.showGrid=true;
	set scaleAxis.significantDigits=4;
	set scaleBar.automaticScale=true;
	set scaleBar.fontSize=10.0;
	set scaleBar.isShown=true;
	set scaleBar.lineWidth=1.0;
	set scaleBar.scaleRange=0.0;
	set scaleBar.significantDigits=4;
	set tipLabels.colorAttribute="User Selection";
	set tipLabels.displayAttribute="Names";
	set tipLabels.fontName="Arial";
	set tipLabels.fontSize=10;
	set tipLabels.fontStyle=0;
	set tipLabels.isShown=true;
	set tipLabels.significantDigits=4;
	set trees.order=true;
	set trees.orderType="increasing";
	set trees.rooting=false;
	set trees.rootingType="User Selection";
	set trees.transform=false;
	set trees.transformType="cladogram";
end;
\ No newline at end of file
diff -r 2040cda75d1f -r 661b74ba4cc8 test-data/dummy.nwk
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dummy.nwk	Fri Feb 03 15:26:41 2017 -0500
@@ -0,0 +1,1 @@
+(((seq1:0.001,seq2:0.002):0.001,seq3:0.005):0.004,seq4:0.003):0.001;