Mercurial > repos > abims-sbr > pogs

changeset 8:3fbf4e4d111e draft

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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 17acd02c547bd1f7661a846661aa99de9743efe9
author abims-sbr
date Tue, 27 Feb 2018 08:41:45 -0500
parents 04422117fcd7
children a76e4758dc44
files POGs.xml adaptsearch_picture_helps.png static/images/adaptsearch_picture_helps.png test-data/2_pogs.output
diffstat 4 files changed, 68 insertions(+), 15 deletions(-) [+]
line wrap: on
line diff
--- 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.
 
 --------
Binary file adaptsearch_picture_helps.png has changed
Binary file static/images/adaptsearch_picture_helps.png has changed
--- /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
+