# HG changeset patch
# User abims-sbr
# Date 1519738905 18000
# Node ID 3fbf4e4d111edd09ef6aba4eae22334ebd92dcbd
# Parent  04422117fcd7d9bbf3d780f7a353442206515f76
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 17acd02c547bd1f7661a846661aa99de9743efe9

diff -r 04422117fcd7 -r 3fbf4e4d111e POGs.xml
--- a/POGs.xml	Wed Jan 17 11:31:30 2018 -0500
+++ b/POGs.xml	Tue Feb 27 08:41:45 2018 -0500
@@ -16,19 +16,19 @@
 
   	<command>
 	<![CDATA[
-        #set $infiles_from_paiwise_prot = ""
-        #for $input_from_paiwise_prot in $inputs_from_paiwise_prot
-            ln -s '$input_from_paiwise_prot' '$input_from_paiwise_prot.element_identifier';
-            #set $infiles_from_paiwise_prot = $infiles_from_paiwise_prot + $input_from_paiwise_prot.element_identifier + ","
+        #set $infiles_from_paiwise_dna = ""
+        #for $input_from_paiwise_dna in $inputs_from_paiwise_dna
+            ln -s '$input_from_paiwise_dna' '$input_from_paiwise_dna.element_identifier';
+            #set $infiles_from_paiwise_dna = $infiles_from_paiwise_dna + $input_from_paiwise_dna.element_identifier + ","
         #end for
-        #set $infiles_from_paiwise_prot = $infiles_from_paiwise_prot[:-1]
+        #set $infiles_from_paiwise_dna = $infiles_from_paiwise_dna[:-1]
 
-		python '$__tool_directory__/scripts/pogs.py' '$infiles_from_paiwise_prot' '$minspec' 
+		python '$__tool_directory__/scripts/pogs.py' '$infiles_from_paiwise_dna' '$minspec' 
         
-        #if '$verbose':
+        #if $verbose=="T":
             -v
         #end if
-        #if '$paralogs':
+        #if $paralogs=="T":
             -p
         #end if
 
@@ -38,7 +38,7 @@
   	</command>
 
  	<inputs>
-        <param name="inputs_from_paiwise_prot" type="data" format="fasta" multiple="true" label="Input files from Pairwise Prot" />
+        <param name="inputs_from_paiwise_dna" type="data" format="fasta" multiple="true" label="Input files from Pairwise DNA" />
 		<param name="minspec" type="integer" value="3" label="Drop orthogroups with less than n species" />	
         <param name="verbose" type="boolean" checked="True" truevalue="T" falsevalue="F" label="Verbose" help="Display a summary table of orthogroups before paralogs filtering"/>
         <param name="paralogs" type="boolean" checked="False" truevalue="T" falsevalue="F" label="Paralogs" help="Return also orthogroups without paralogs filtering"/>
@@ -57,7 +57,7 @@
 
 	<tests>
 		<test>
-            <param name="inputs_from_paiwise_prot" ftype="fasta" value="output_pairwise/RBH_AmAmphi_AcAcaud.fasta,output_pairwise/RBH_ApApomp_AcAcaud.fasta,output_pairwise/RBH_ApApomp_AmAmphi.fasta,output_pairwise/RBH_TeTerlap_AcAcaud.fasta,output_pairwise/RBH_TeTerlap_AmAmphi.fasta,output_pairwise/RBH_TeTerlap_ApApomp.fasta"/>
+            <param name="inputs_from_paiwise_dna" ftype="fasta" value="output_pairwise/RBH_AmAmphi_AcAcaud.fasta,output_pairwise/RBH_ApApomp_AcAcaud.fasta,output_pairwise/RBH_ApApomp_AmAmphi.fasta,output_pairwise/RBH_TeTerlap_AcAcaud.fasta,output_pairwise/RBH_TeTerlap_AmAmphi.fasta,output_pairwise/RBH_TeTerlap_ApApomp.fasta"/>
 			<param name="minspec" value="3"/>
             <param name="verbose" value="True"/>
             <param name="paralogs" value="True"/>
@@ -87,6 +87,25 @@
                 <element name="orthogroup_10_with_4_sequences_withParalogs" value="outputs_withParalogs/orthogroup_10_with_4_sequences_withParalogs.fasta" />
             </output_collection>
 		</test>
+        <test>
+            <param name="inputs_from_paiwise_dna" ftype="fasta" value="output_pairwise/RBH_AmAmphi_AcAcaud.fasta,output_pairwise/RBH_ApApomp_AcAcaud.fasta,output_pairwise/RBH_ApApomp_AmAmphi.fasta,output_pairwise/RBH_TeTerlap_AcAcaud.fasta,output_pairwise/RBH_TeTerlap_AmAmphi.fasta,output_pairwise/RBH_TeTerlap_ApApomp.fasta"/>
+            <param name="minspec" value="3"/>
+            <param name="verbose" value="True"/>
+            <param name="paralogs" value="False"/>
+            <output name="log" value="2_pogs.output" />
+            <output_collection name="output" type="list">
+                <element name="orthogroup_1_with_4_sequences" value="outputs/orthogroup_1_with_4_sequences.fasta" />
+                <element name="orthogroup_2_with_4_sequences" value="outputs/orthogroup_2_with_4_sequences.fasta" />
+                <element name="orthogroup_3_with_3_sequences" value="outputs/orthogroup_3_with_3_sequences.fasta" />
+                <element name="orthogroup_4_with_4_sequences" value="outputs/orthogroup_4_with_4_sequences.fasta" />
+                <element name="orthogroup_5_with_3_sequences" value="outputs/orthogroup_5_with_3_sequences.fasta" />
+                <element name="orthogroup_6_with_4_sequences" value="outputs/orthogroup_6_with_4_sequences.fasta" />
+                <element name="orthogroup_7_with_3_sequences" value="outputs/orthogroup_7_with_3_sequences.fasta" />
+                <element name="orthogroup_8_with_3_sequences" value="outputs/orthogroup_8_with_3_sequences.fasta" />
+                <element name="orthogroup_9_with_3_sequences" value="outputs/orthogroup_9_with_3_sequences.fasta" />
+                <element name="orthogroup_10_with_3_sequences" value="outputs/orthogroup_10_with_3_sequences.fasta" />
+            </output_collection>
+        </test>
 	</tests>	
 
 	<help>
@@ -105,17 +124,19 @@
 
 **Inputs**
 
-The output (nucleic format) of the tool 'Pairwise' (AdaptSearch suite), which consists in lists of homologous sequences between pairs of species obtained by RBH comparisons.
+The output of the tool 'Pairwise' (pairwise_DNA, nucleic format) (AdaptSearch suite), which consists in lists of homologous sequences between pairs of species obtained by RBH comparisons.
 
 --------
 
 **Parameters**
 
-** Species minimum ** : drop orthogroups with less than n species : orthogroups with less than n species within won't be recorded.
-** verbose ** : check 'Yes' if you want a supplementary table : countings of orthogroups before the paralogous sequences removal
-** paralogs ** : check 'yes' if you also want to retrieve the orthogroups before the paralogous sequences removal
+- Species minimum : drop orthogroups with less than n species : orthogroups with less than n species within won't be recorded.
+
+- verbose : check 'Yes' if you want a supplementary table : countings of orthogroups before the paralogous sequences removal.
 
-.. class:: warningmark
+- paralogs : check 'Yes' if you also want to retrieve the orthogroups before the paralogous sequences removal.
+
+:: .. class:: warningmark
 The minimum number of species per group only applies to the main output files. In the case of the 'paralogs' option, this parameter is more likely the minimum amount of sequences to keep.
 
 --------
diff -r 04422117fcd7 -r 3fbf4e4d111e adaptsearch_picture_helps.png
Binary file adaptsearch_picture_helps.png has changed
diff -r 04422117fcd7 -r 3fbf4e4d111e static/images/adaptsearch_picture_helps.png
Binary file static/images/adaptsearch_picture_helps.png has changed
diff -r 04422117fcd7 -r 3fbf4e4d111e test-data/2_pogs.output
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/2_pogs.output	Tue Feb 27 08:41:45 2018 -0500
@@ -0,0 +1,32 @@
+*** pogs.py ***
+
+Building of orthogroups based on pairs of genes obtained by pairwise comparisons between pairs of species.
+Genes are gathered in orthogroups based on the principle of transitivity between genes pairs.
+
+Parsing input files ...
+Creating Orthogroups ...
+
+    Summary before paralogous filtering : 
+
+         2 sps  3 sps  4 sps
+2 seqs    1394      0      0
+3 seqs       0    163      0
+4 seqs       0     26     33
+5 seqs       0      3     17
+6 seqs       0      0     17
+7 seqs       0      0      7
+8 seqs       0      0      2
+11 seqs      0      0      1
+13 seqs      0      0      1 
+
+Filtering paralogous sequences and writing final orthogroups files ...
+    (Dropping Orthogroups with less than 3 species)
+
+    Summary after paralogous filtering : 
+
+        3 sps  4 sps
+3 seqs    192      0
+4 seqs      0     78
+
+270 orthogroups have been infered from 6 pairwise comparisons by RBH
+