# HG changeset patch
# User abims-sbr
# Date 1530629720 14400
# Node ID ff1a3a7903636f253a0377d6df74078f638a2d2c
# Parent  ad3446d7f79416e9fd5f1c283436fc348d52006c
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit f1ba8d136e0129f3e8435b25a95f70f697d51464-dirty

diff -r ad3446d7f794 -r ff1a3a790363 ConcatPhyl.xml
--- a/ConcatPhyl.xml	Fri Mar 16 05:09:42 2018 -0400
+++ b/ConcatPhyl.xml	Tue Jul 03 10:55:20 2018 -0400
@@ -20,15 +20,13 @@
             #set $infiles_filter_assemblies = $infiles_filter_assemblies + $input_filter_assemblie.element_identifier + ","
         #end for
         #set $infiles_filter_assemblies = $infiles_filter_assemblies[:-1]
-
-        #set $infiles_alignments = ""
+        
         #for $input_alignment in $input_alignments
             ln -s '$input_alignment' '$input_alignment.element_identifier';
-            #set $infiles_alignments = $infiles_alignments + $input_alignment.element_identifier + ","
-        #end for
-        #set $infiles_alignments = $infiles_alignments[:-1]
+            echo '$input_alignment.element_identifier' >> list_files;            
+        #end for        
 
-        python $__tool_directory__/scripts/S01_concatenate.py
+        python $__tool_directory__/scripts/S01_concatenate.py 
 
         $infiles_filter_assemblies
 
@@ -38,7 +36,8 @@
             proteic
         #end if
 
-        $infiles_alignments
+        list_files
+        
         > ${output};
 
         raxmlHPC -n galaxy_run
@@ -215,7 +214,7 @@
 	<tests>
 		<test>
             <param name="input_filter_assemblies" ftype="fasta" value="input_filter_assemblies/AcAcaud_trinity.fasta,input_filter_assemblies/AmAmphi_trinity.fasta,input_filter_assemblies/ApApomp_trinity.fasta,input_filter_assemblies/PgPgras_trinity.fasta,input_filter_assemblies/PhPhess_trinity.fasta,input_filter_assemblies/ThThelep_trinity.fasta" />
-            <param name="input_alignments" ftype="fasta" value="input_from_CDS_Search/locus17_sp3_sp3.fasta,input_from_CDS_Search/locus147_sp3_sp3.fasta,input_from_CDS_Search/locus183_sp3_sp3.fasta,input_from_CDS_Search/locus334_sp3_sp3.fasta" />
+            <param name="input_alignments" ftype="fasta" value="input_from_CDS_Search/orthogroup_17_sp3_sp3.fasta,input_from_CDS_Search/orthogroup_147_sp3_sp3.fasta,input_from_CDS_Search/orthogroup_183_sp3_sp3.fasta,input_from_CDS_Search/orthogroup_334_sp3_sp3.fasta" />
             <conditional name="format">
 				<param name="format_run" value="nucleic" />
 				<param name="base_model" value="GTRGAMMA" />
@@ -241,7 +240,7 @@
 
         <test>
             <param name="input_filter_assemblies" ftype="fasta" value="input_filter_assemblies/AcAcaud_trinity.fasta,input_filter_assemblies/AmAmphi_trinity.fasta,input_filter_assemblies/ApApomp_trinity.fasta,input_filter_assemblies/PgPgras_trinity.fasta,input_filter_assemblies/PhPhess_trinity.fasta,input_filter_assemblies/ThThelep_trinity.fasta" />
-            <param name="input_alignments" ftype="fasta" value="input_from_CDS_Search/locus17_sp3_sp3.fasta,input_from_CDS_Search/locus147_sp3_sp3.fasta,input_from_CDS_Search/locus183_sp3_sp3.fasta,input_from_CDS_Search/locus334_sp3_sp3.fasta" />
+            <param name="input_alignments" ftype="fasta" value="input_from_CDS_Search/orthogroup_17_sp3_sp3.fasta,input_from_CDS_Search/orthogroup_147_sp3_sp3.fasta,input_from_CDS_Search/orthogroup_183_sp3_sp3.fasta,input_from_CDS_Search/orthogroup_334_sp3_sp3.fasta" />
             <conditional name="format">
                 <param name="format_run" value="nucleic" />
                 <param name="base_model" value="GTRGAMMA" />
@@ -261,7 +260,7 @@
         
         <test>
             <param name="input_filter_assemblies" ftype="fasta" value="input_filter_assemblies/AcAcaud_trinity.fasta,input_filter_assemblies/AmAmphi_trinity.fasta,input_filter_assemblies/ApApomp_trinity.fasta,input_filter_assemblies/PgPgras_trinity.fasta,input_filter_assemblies/PhPhess_trinity.fasta,input_filter_assemblies/ThThelep_trinity.fasta" />
-            <param name="input_alignments" ftype="fasta" value="input_from_CDS_Search/locus17_sp3_sp3.fasta,input_from_CDS_Search/locus147_sp3_sp3.fasta,input_from_CDS_Search/locus183_sp3_sp3.fasta,input_from_CDS_Search/locus334_sp3_sp3.fasta" />
+            <param name="input_alignments" ftype="fasta" value="input_from_CDS_Search/orthogroup_17_sp3_sp3.fasta,input_from_CDS_Search/orthogroup_147_sp3_sp3.fasta,input_from_CDS_Search/orthogroup_183_sp3_sp3.fasta,input_from_CDS_Search/orthogroup_334_sp3_sp3.fasta" />
             <conditional name="format">
                 <param name="format_run" value="nucleic" />
                 <param name="base_model" value="GTRGAMMA" />
diff -r ad3446d7f794 -r ff1a3a790363 scripts/S01_concatenate.py
--- a/scripts/S01_concatenate.py	Fri Mar 16 05:09:42 2018 -0400
+++ b/scripts/S01_concatenate.py	Tue Jul 03 10:55:20 2018 -0400
@@ -129,7 +129,6 @@
 ## Arguments
 infiles_filter_assemblies = sys.argv[1]
 format_run = sys.argv[2]
-input_alignments = sys.argv[3]
 
 ## add file to list_species
 list_species = str.split(infiles_filter_assemblies,",")
@@ -140,7 +139,16 @@
     SPECIES_ID_LIST.append(name)
 
 ## add alignment files to L_IN
-L_IN = str.split(input_alignments,",")
+list_files = []
+with open(sys.argv[3], 'r') as f:
+    for line in f.readlines():
+        list_files.append(line.strip('\n'))
+
+L_IN = []
+for file in list_files:
+    L_IN.append(file)
+
+#L_IN = str.split(input_alignments,",")
 print(L_IN)
 
 ### 1 ### Proteic
diff -r ad3446d7f794 -r ff1a3a790363 static/images/adaptsearch_picture_helps.png
Binary file static/images/adaptsearch_picture_helps.png has changed
diff -r ad3446d7f794 -r ff1a3a790363 test-data/input_from_CDS_Search/locus147_sp3_sp3.fasta
--- a/test-data/input_from_CDS_Search/locus147_sp3_sp3.fasta	Fri Mar 16 05:09:42 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
->Ph48961/110
-------------------------------------------------------------ttagttacctcggcttttactgtctgtggcgtcgattctacaaacttctttgcctgtacaagattcatgccagccataacattctttatctgtttaataagagctactttcttggcttcatcaaaaccagcaagtttaacggtaaatgccaccttttctggcttcttctctgatggcgtttcctcgtcttcctttggagcaatagccggcatggctcccatggccatcataggagtgtctgtaatgttcagtgttttttttaataac------------------------------------------------------------------------
->Ap66541/110
-tccacttctatctttcctcctactgcctctaaagctttcttcaaagcctctgcttcctctttagttacctcggcttttactgtctgtggacttgattctacaaatttctttgcctgtacaagattcattccaggcatcacattctttatctcctttataagtgctactttctttgcttcatcaaaaccagtaagttttacagtaaatgccactttttctggtttcttctctgctggttcttcttcctctgccttggcagcaacagcaggcatggctcccatggccatcattggagtgtctgtgattttcagtgttttctttaataactcgtttaaatctgctacttctattagggtcagtttactaatctcatcaacaaggttctgtattttttcaggg
->Ac62411/110
-tccacttctatctttcctccgactgcctctaaagctttcttcaaagcctctgcttcttctttagttacctcggcttttactgtctgtggacttgactctacaaatttctttgcttgtacaagattcattccaggcatcacgttctttatctcctttatgagtgctactttcttggcttcatcaaaaccagtaagttttacagtaaatgccactttttctggtttcttctctgctggttcttcatcctctgccttggcagcaacagcaggcatggctcccatggccatcattggagtgtctgtgatgttgagtgttttctttaataactcgtttaaatctgctacttctattagtgtcagtttactaatctcatcaacaaggttctgtattttttcaggg
diff -r ad3446d7f794 -r ff1a3a790363 test-data/input_from_CDS_Search/locus17_sp3_sp3.fasta
--- a/test-data/input_from_CDS_Search/locus17_sp3_sp3.fasta	Fri Mar 16 05:09:42 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
->Ac28231/110
-atggatcaggtaatgcagttcattgagccagccaggcagtttgccaaggattccatccgactggtgaaaaggtgtacgaagccagatagaagagagttccagaagatagccatggccactgctattggttttgccatcatgggatttattggcttctttgtaaagctcatccacataccaatcaataatatcattgtgggttc?
->Am49621/110
-atggatcaggttgtgcagtttgtcgagccggcaaagcagtttgcgaaggactccatccgattggtgaaaagatgcaccaagccagatcgcaaagaatttcagaagattgccatggcgactgcgataggatttgctatcatgggtttcatcggattctttgtcaaattaatccacattcccatcaacaacatcatcgtaggttca
->Pg54991/110
-------------------------gagccagcaaagcagtttgcaaaagattctatacgactggttaaaagatgcaccaaaccagatagaagagaattccagaagatagccatggcaactgctattggttttgctattatggggtttatcggatttttcgttaagctgatccatataccaatcaacaacatcattgtgggttcc
diff -r ad3446d7f794 -r ff1a3a790363 test-data/input_from_CDS_Search/locus183_sp3_sp3.fasta
--- a/test-data/input_from_CDS_Search/locus183_sp3_sp3.fasta	Fri Mar 16 05:09:42 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
->Th20211/110
-------------------------------gcccgtaagatgaaggaccatcgtcgagaccagaaatggcacgacaaagattacaagaaaagccacttgggtactcgctggaaggccaacgccttcggaggtgcatcccatgccaagggaatcgtgctcgagaaagtaggtgttgaggccaagcagcccaactctgccatccgcaagtgtgtgcgagttcagctgatcaagaacggcaaaaagatcacggccttcgtaccgcgggacggttgtctcaactacattgaggagaacgatgaggtgctgatcgctggattcggacgaaagggccacgctgtcggagatattcccggcgttcgcttcaag------------------------------------------------------------------
->Ap32511/110
-aagatgggcaagcctcatggacttaggacagcccgtaagatgcgggaccaccgccgtgaccagaggtggcatgataaagactacaaaaagagtcatttgggtactcgctggaaggccaatccatttggtggcgcatcccatgctaagggaatcgtcctcgagaaagtaggtgttgaagccaaacagcccaactctgccattcgtaaatgtgtcagagtgcagttgataaaaaatggcaagaaaattactgcttttgtaccaagggacggttgtctgaactacatcgaggagaatgatgaagttctcattgctggatttggtcgtaaaggtcatgctgtaggagatattcctggtgtacgcttcaaggttgttaaagtggcaaatgtgtccctgttggccttgtacaaggagaagaaggaaagaccaaggtct
->Ac8151/1100
-aagatgggcaagcctcacggactcagaacagcccgtaagatgcgggaccaccgccgtgaccagaggtggcatgataaggactacaaaaagagtcacttgggtactcgctggaaggccaatccctttggtggtgcttcccacgccaagggaatcgtcctcgagaaagtaggtgttgaagccaaacagcccaactctgccattcggaaatgtgtcagagtgcagcttataaaaaacggcaagaaaattactgcctttgtaccaagggatggctgtctgaactacattgaggagaatgacgaagttctcattgctggatttggccgtaaaggtcatgctgtaggagatattcctggtgtacgcttcaaggttgttaaagtggcaaacgtatccctgttggctttgtacaaggagaagaaagaaagaccaaggtct
diff -r ad3446d7f794 -r ff1a3a790363 test-data/input_from_CDS_Search/locus334_sp3_sp3.fasta
--- a/test-data/input_from_CDS_Search/locus334_sp3_sp3.fasta	Fri Mar 16 05:09:42 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
->Ap2871/1100
-gaggacttcaccttccttttgctttctagagtctcaatcacattctggtacttccaaccaacctcatgggaaaggcgtccaagaacacagtacttgcgtctagccttcagtctaaggactctcagagctgagggcactaccatgcgtttcttcttgtcatatggaggtggaattccctcaaacaccttcaggtgggacaaagccacctttccacgagtaagcttgtgtggcaacatgccacgcacagttctccagaatatcttgcttggagctcggaagtggaaaggaccacggctcggattagtgttcattcgcttccgcaagaaagccaagtattttaacttgttcctg
->Th30731/110
-------------------------------------------------------------------------------------------------------------------------------------------accatacgcttctgcttgtcatatggaggggggatgccttcaaacactttcattctctccaaagctgccttgccacggggtaacttatgtggcaacattcctctgactgttctccagaaaatcttgctgggagcacggaagtggaatggaccacggcttggtttggtgttcatacgctttctaaggaaatccaagtacttgagt---------
->Pg43701/110
-gtggacttgagctttcttttgttttctaatgtagtgatgacattctggtacttccagcccacttcatgtgacaggcggccaagaacacatgacttgcgtctagctttaagtcgaaggaccttcaaagccgagggaaccaccatacgtttctgcttgtcaaatggtggagggatgccctcaaagaccttgagacggtccagagcttgcttaccacgtgtcagcttatgtggcaacataccacgcacagttctccaaaatattttacttggggcacggaagtggtatgggccacggcttggattggtgttcattcgtttccttaggaaagcaaggtacttcagtttgttcctg
diff -r ad3446d7f794 -r ff1a3a790363 test-data/input_from_CDS_Search/orthogroup_147_sp3_sp3.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input_from_CDS_Search/orthogroup_147_sp3_sp3.fasta	Tue Jul 03 10:55:20 2018 -0400
@@ -0,0 +1,6 @@
+>Ph48961/110
+------------------------------------------------------------ttagttacctcggcttttactgtctgtggcgtcgattctacaaacttctttgcctgtacaagattcatgccagccataacattctttatctgtttaataagagctactttcttggcttcatcaaaaccagcaagtttaacggtaaatgccaccttttctggcttcttctctgatggcgtttcctcgtcttcctttggagcaatagccggcatggctcccatggccatcataggagtgtctgtaatgttcagtgttttttttaataac------------------------------------------------------------------------
+>Ap66541/110
+tccacttctatctttcctcctactgcctctaaagctttcttcaaagcctctgcttcctctttagttacctcggcttttactgtctgtggacttgattctacaaatttctttgcctgtacaagattcattccaggcatcacattctttatctcctttataagtgctactttctttgcttcatcaaaaccagtaagttttacagtaaatgccactttttctggtttcttctctgctggttcttcttcctctgccttggcagcaacagcaggcatggctcccatggccatcattggagtgtctgtgattttcagtgttttctttaataactcgtttaaatctgctacttctattagggtcagtttactaatctcatcaacaaggttctgtattttttcaggg
+>Ac62411/110
+tccacttctatctttcctccgactgcctctaaagctttcttcaaagcctctgcttcttctttagttacctcggcttttactgtctgtggacttgactctacaaatttctttgcttgtacaagattcattccaggcatcacgttctttatctcctttatgagtgctactttcttggcttcatcaaaaccagtaagttttacagtaaatgccactttttctggtttcttctctgctggttcttcatcctctgccttggcagcaacagcaggcatggctcccatggccatcattggagtgtctgtgatgttgagtgttttctttaataactcgtttaaatctgctacttctattagtgtcagtttactaatctcatcaacaaggttctgtattttttcaggg
diff -r ad3446d7f794 -r ff1a3a790363 test-data/input_from_CDS_Search/orthogroup_17_sp3_sp3.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input_from_CDS_Search/orthogroup_17_sp3_sp3.fasta	Tue Jul 03 10:55:20 2018 -0400
@@ -0,0 +1,6 @@
+>Ac28231/110
+atggatcaggtaatgcagttcattgagccagccaggcagtttgccaaggattccatccgactggtgaaaaggtgtacgaagccagatagaagagagttccagaagatagccatggccactgctattggttttgccatcatgggatttattggcttctttgtaaagctcatccacataccaatcaataatatcattgtgggttc?
+>Am49621/110
+atggatcaggttgtgcagtttgtcgagccggcaaagcagtttgcgaaggactccatccgattggtgaaaagatgcaccaagccagatcgcaaagaatttcagaagattgccatggcgactgcgataggatttgctatcatgggtttcatcggattctttgtcaaattaatccacattcccatcaacaacatcatcgtaggttca
+>Pg54991/110
+------------------------gagccagcaaagcagtttgcaaaagattctatacgactggttaaaagatgcaccaaaccagatagaagagaattccagaagatagccatggcaactgctattggttttgctattatggggtttatcggatttttcgttaagctgatccatataccaatcaacaacatcattgtgggttcc
diff -r ad3446d7f794 -r ff1a3a790363 test-data/input_from_CDS_Search/orthogroup_183_sp3_sp3.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input_from_CDS_Search/orthogroup_183_sp3_sp3.fasta	Tue Jul 03 10:55:20 2018 -0400
@@ -0,0 +1,6 @@
+>Th20211/110
+------------------------------gcccgtaagatgaaggaccatcgtcgagaccagaaatggcacgacaaagattacaagaaaagccacttgggtactcgctggaaggccaacgccttcggaggtgcatcccatgccaagggaatcgtgctcgagaaagtaggtgttgaggccaagcagcccaactctgccatccgcaagtgtgtgcgagttcagctgatcaagaacggcaaaaagatcacggccttcgtaccgcgggacggttgtctcaactacattgaggagaacgatgaggtgctgatcgctggattcggacgaaagggccacgctgtcggagatattcccggcgttcgcttcaag------------------------------------------------------------------
+>Ap32511/110
+aagatgggcaagcctcatggacttaggacagcccgtaagatgcgggaccaccgccgtgaccagaggtggcatgataaagactacaaaaagagtcatttgggtactcgctggaaggccaatccatttggtggcgcatcccatgctaagggaatcgtcctcgagaaagtaggtgttgaagccaaacagcccaactctgccattcgtaaatgtgtcagagtgcagttgataaaaaatggcaagaaaattactgcttttgtaccaagggacggttgtctgaactacatcgaggagaatgatgaagttctcattgctggatttggtcgtaaaggtcatgctgtaggagatattcctggtgtacgcttcaaggttgttaaagtggcaaatgtgtccctgttggccttgtacaaggagaagaaggaaagaccaaggtct
+>Ac8151/1100
+aagatgggcaagcctcacggactcagaacagcccgtaagatgcgggaccaccgccgtgaccagaggtggcatgataaggactacaaaaagagtcacttgggtactcgctggaaggccaatccctttggtggtgcttcccacgccaagggaatcgtcctcgagaaagtaggtgttgaagccaaacagcccaactctgccattcggaaatgtgtcagagtgcagcttataaaaaacggcaagaaaattactgcctttgtaccaagggatggctgtctgaactacattgaggagaatgacgaagttctcattgctggatttggccgtaaaggtcatgctgtaggagatattcctggtgtacgcttcaaggttgttaaagtggcaaacgtatccctgttggctttgtacaaggagaagaaagaaagaccaaggtct
diff -r ad3446d7f794 -r ff1a3a790363 test-data/input_from_CDS_Search/orthogroup_334_sp3_sp3.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input_from_CDS_Search/orthogroup_334_sp3_sp3.fasta	Tue Jul 03 10:55:20 2018 -0400
@@ -0,0 +1,6 @@
+>Ap2871/1100
+gaggacttcaccttccttttgctttctagagtctcaatcacattctggtacttccaaccaacctcatgggaaaggcgtccaagaacacagtacttgcgtctagccttcagtctaaggactctcagagctgagggcactaccatgcgtttcttcttgtcatatggaggtggaattccctcaaacaccttcaggtgggacaaagccacctttccacgagtaagcttgtgtggcaacatgccacgcacagttctccagaatatcttgcttggagctcggaagtggaaaggaccacggctcggattagtgttcattcgcttccgcaagaaagccaagtattttaacttgttcctg
+>Th30731/110
+------------------------------------------------------------------------------------------------------------------------------------------accatacgcttctgcttgtcatatggaggggggatgccttcaaacactttcattctctccaaagctgccttgccacggggtaacttatgtggcaacattcctctgactgttctccagaaaatcttgctgggagcacggaagtggaatggaccacggcttggtttggtgttcatacgctttctaaggaaatccaagtacttgagt---------
+>Pg43701/110
+gtggacttgagctttcttttgttttctaatgtagtgatgacattctggtacttccagcccacttcatgtgacaggcggccaagaacacatgacttgcgtctagctttaagtcgaaggaccttcaaagccgagggaaccaccatacgtttctgcttgtcaaatggtggagggatgccctcaaagaccttgagacggtccagagcttgcttaccacgtgtcagcttatgtggcaacataccacgcacagttctccaaaatattttacttggggcacggaagtggtatgggccacggcttggattggtgttcattcgtttccttaggaaagcaaggtacttcagtttgttcctg