Merge branch 'dev'

.gitignore

@@ -0,0 +1,2 @@
+tool_test_output.html
+tool_test_output.json

galaxy_wrappers/01_Filter_Assemblies/filter_assembly.xml

@@ -18,17 +18,17 @@
 
   	<command>
 	<![CDATA[
-		ln -s $__tool_directory__/01_Choose_One_variants_per_locus_TRINITY_v1.0.py .
+		ln -s $__tool_directory__/scripts/S02a_remove_redondancy_from_velvet_oases.py .
 		&&
-		ln -s $__tool_directory__/02_format_fasta_name_TRINITY.py .
+		ln -s $__tool_directory__/scripts/S02b_format_fasta_name_trinity.py .
 		&&
-		ln -s $__tool_directory__/filter.py .
+		ln -s $__tool_directory__/scripts/S03_choose_one_variants_per_locus_trinity.py .
 		&&
-		ln -s $__tool_directory__/find_orf.py .
+		ln -s $__tool_directory__/scripts/S04_find_orf.py .
 		&&
-		ln -s $__tool_directory__/remove_redondancy_from_oases_output_v3.1.py .
+		ln -s $__tool_directory__/scripts/S05_filter.py .
 		&&
-		python $__tool_directory__/script_to_choose.py
+		python $__tool_directory__/scripts/S01_script_to_choose.py
 
 		#if $input.input_type_choice == "velvet"
 			velvet ${input.zip_velvet} 

galaxy_wrappers/01_Filter_Assemblies/scripts

@@ -0,0 +1 @@
+../../scripts/01_Filter_Assemblies/

galaxy_wrappers/02_Pairwise/pairwise.xml

@@ -18,31 +18,31 @@
 
   	<command>
         	<![CDATA[
-        ln -s $__tool_directory__/03_run_BLAST_with.K.filter.sh .
+        ln -s $__tool_directory__/scripts/S02_xxx_patron_pipeline.sh .
         &&        
-        ln -s $__tool_directory__/05_scriptExtractMatch_v20_BLASTX.py .
+        ln -s $__tool_directory__/scripts/S03_run_blast_with_k_filter.sh .
         &&
-        ln -s $__tool_directory__/08_1_postProcessing_of_pairwise_v3.0.py .
+        ln -s $__tool_directory__/scripts/S04_run_blast2_with_k_filter.sh .
         &&
-        ln -s $__tool_directory__/08_2_formatMatch_getBackNucleotides_v2.py .
+        ln -s $__tool_directory__/scripts/S05_script_extract_match_v20_blastx.py .
         &&
-        ln -s $__tool_directory__/10_run_BLAST2_with.K.filter.sh .        
+        ln -s $__tool_directory__/scripts/S06_post_processing_of_pairwise.py .        
         && 
-        ln -s $__tool_directory__/12_scriptExtractMatch_v20_BLASTX.py .
+        ln -s $__tool_directory__/scripts/S07_format_match_get_back_nucleotides.py .
         &&
-        ln -s $__tool_directory__/14_postProcessing_of_pairwise_v3.0.py .
+        ln -s $__tool_directory__/scripts/S08_script_extract_match_v20_blastx.py .
         &&
-        ln -s $__tool_directory__/16_compareListPairs_forReciprocalBestHitsTest_v3.1.py .
+        ln -s $__tool_directory__/scripts/S09_post_processing_of_pairwise.py .
         &&
-        ln -s $__tool_directory__/18_postProcessing_of_pairwise_v4.0.py .
+        ln -s $__tool_directory__/scripts/S10_compare_list_pairs_for_reciprocal_best_hits_test.py .
         &&
-        ln -s $__tool_directory__/24_PROT2DNA_v2.2.py .
+        ln -s $__tool_directory__/scripts/S11_post_processing_of_pairwise.py .
         &&
-        ln -s $__tool_directory__/XXX_patronPipeline.sh .
+        ln -s $__tool_directory__/scripts/S12_prot2dna.py .
         &&
-        ln -s $__tool_directory__/zip.py .
+        ln -s $__tool_directory__/scripts/S13_zip.py .
         &&
-		python $__tool_directory__/03_organize_RBH.py 8 ${e_value} ${zip}
+		python $__tool_directory__/scripts/S01_organize_rbh.py 8 ${e_value} ${zip}
 		> ${output};
 		]]>
   	</command>

galaxy_wrappers/02_Pairwise/scripts

@@ -0,0 +1 @@
+../../scripts/02_Pairwise/

galaxy_wrappers/03_POGs/POGs.xml

@@ -15,10 +15,10 @@
 
   	<command>
 	<![CDATA[
-		python $__tool_directory__/01_get_locus_ortholog_part1.py ${zip_file}
+		python $__tool_directory__/scripts/S01_get_locus_ortholog_part1.py ${zip_file}
 		> ${output} &&
 
-		python $__tool_directory__/03_get_locus_ortholog_part2.py ${zip}
+		python $__tool_directory__/scripts/S02_get_locus_ortholog_part2.py ${zip}
 		>> ${output};
 	]]>
   	</command>

galaxy_wrappers/03_POGs/scripts

@@ -0,0 +1 @@
+../../scripts/03_POGs

galaxy_wrappers/04_BlastAlign/BlastAlign.xml

@@ -11,25 +11,22 @@
 	</macros>
 
 	<requirements>
-		<expand macro="python_required" />
-		<requirement type="package" version="5.20.3">perl</requirement>
-		<requirement type="package" >blast-legacy</requirement>
+	    <expand macro="python_required" />
+		<requirement type="package" version="5.22.0">perl</requirement>
+		<requirement type="package" >blast-legacy</requirement>		
+		<requirement type="package" version="1.4">blastalign</requirement>
 	</requirements>
 
 	<stdio>
         <exit_code range="1:" level="fatal" />
     </stdio>
 
   	<command>
-	<![CDATA[
-		ln -s $__tool_directory__/BlastAlign.py .
-		&&
-		ln -s $__tool_directory__/phylip2fasta.py .
-		&&
-		ln -s $__tool_directory__/BlastALign .
+	<![CDATA[		
+		ln -s $__tool_directory__/scripts/S02_phylip2fasta.py .		
 		&&
 		#if $files.type == "one" :
-			$__tool_directory__/BlastAlign -i ${files.one_file} -o out
+			BlastAlign -i ${files.one_file} -o out
 			#if $files.options.option == "yes" :
 				#if $files.options.options_m.m == True :
 					-m ${files.options.options_m.proportion}
@@ -55,12 +52,12 @@
 			#end if
 			>${outfile};
 			#if $fasta_out.value == True :
-				python $__tool_directory__/phylip2fasta.py out.phy out.fasta >>${outfile};
+				python $__tool_directory__/scripts/S02_phylip2fasta.py out.phy out.fasta >>${outfile};
 			#end if			
 		#end if
 			
 		#if $files.type == "many" :
-			python $__tool_directory__/24_prepare_BlastAlignRuns.py ${files.many_files} 
+			python $__tool_directory__/scripts/S01_prepare_BlastAlign_runs.py ${files.many_files} 
 			#if $fasta_out.value == True :
 				oui
 			#else :

galaxy_wrappers/04_BlastAlign/scripts

@@ -0,0 +1 @@
+../../scripts/04_BlastAlign

galaxy_wrappers/05_CDS_search/CDS_search.xml

@@ -16,15 +16,15 @@
 
   	<command>
   	<![CDATA[
-		python $__tool_directory__/03_findORF_onMultipleAlignment_v2.py ${input_file}  $__tool_directory__/02_input_code_universel_modified.txt
+		python $__tool_directory__/scripts/S01_find_orf_on_multiple_alignment.py ${input_file}  $__tool_directory__/scripts/code_universel_modified.txt
 		#if $lenght.lenght_CDS == "yes" :
 			${lenght.min_lenght_seq}
 		#else :
 			50
 		#end if
 		>${output};
 
-		python $__tool_directory__/01_RemoveTooShort_bit_or_whole_sequence_v1.0.py ${nb_species_keep}
+		python $__tool_directory__/scripts/S02_remove_too_short_bit_or_whole_sequence.py ${nb_species_keep}
 		#if $methionine.value == "yes" :
 			oui
 		#else :
@@ -37,7 +37,7 @@
 		#end if
 		>>${output};
 
-		python $__tool_directory__/07_removeSiteWithNotEnoughSpeciesRepresented_v2.0.py ${nb_species_keep}
+		python $__tool_directory__/scripts/S03_remove_site_with_not_enough_species_represented.py ${nb_species_keep}
 		#if $lenght.lenght_CDS == "yes" :
 			${lenght.min_lenght_nuc}
 		#else :
@@ -139,7 +139,7 @@
 			<param name="out_BESTORF" value="no" />
 			<param name="out_CDS" value="no" />
 			<param name="out_CDS_filter" value="nuc" />
-			<output name="output" value="test_08.out" />	<!-- test_08.out ? -->		
+			<output name="output" value="test_08.out" />
 		</test>
 	</tests>
 

galaxy_wrappers/05_CDS_search/CDS_search.xml~

@@ -16,15 +16,15 @@
 
   	<command>
   	<![CDATA[
-		python $__tool_directory__/03_findORF_onMultipleAlignment_v2.py ${input_file}  $__tool_directory__/02_input_code_universel_modified.txt
+		python $__tool_directory__/T5S01a_find_orf_on_multiple_alignment_v2.py ${input_file}  $__tool_directory__/T5S01b_input_code_universel_modified.txt
 		#if $lenght.lenght_CDS == "yes" :
 			${lenght.min_lenght_seq}
 		#else :
 			50
 		#end if
 		>${output};
 
-		python $__tool_directory__/01_RemoveTooShort_bit_or_whole_sequence_v1.0.py ${nb_species_keep}
+		python $__tool_directory__/T5S02_remove_too_short_bit_or_whole_sequence_v1.0.py ${nb_species_keep}
 		#if $methionine.value == "yes" :
 			oui
 		#else :
@@ -37,7 +37,7 @@
 		#end if
 		>>${output};
 
-		python $__tool_directory__/07_removeSiteWithNotEnoughSpeciesRepresented_v2.0.py ${nb_species_keep}
+		python $__tool_directory__/T5S03_remove_site_with_not_enough_species_represented_v2.0.py ${nb_species_keep}
 		#if $lenght.lenght_CDS == "yes" :
 			${lenght.min_lenght_nuc}
 		#else :
@@ -132,14 +132,14 @@
 
 	<tests>
 		<test>
-			<param name="input_file" ftype="zip" value="test_05_input_CDS_Search.zip" />
+			<param name="input_file" ftype="zip" value="test_05_input_CDS_Search.no_unzip.zip" />
 			<param name="nb_species_keep" value="2" />
 			<param name="methionine" value="yes" />
 			<param name="lenght_CDS" value="no" />
 			<param name="out_BESTORF" value="no" />
 			<param name="out_CDS" value="no" />
 			<param name="out_CDS_filter" value="nuc" />
-			<output name="output" value="test_05.out" />	<!-- test_08.out ? -->		
+			<output name="output" value="test_08.out" />
 		</test>
 	</tests>
 

galaxy_wrappers/05_CDS_search/scripts

@@ -0,0 +1 @@
+../../scripts/05_CDS_search

galaxy_wrappers/06_ConcatPhyl/ConcatPhyl.xml

@@ -15,7 +15,7 @@
 	</requirements>
 
   	<command><![CDATA[
-		python $__tool_directory__/01_concatenate_v3.0.py ${zip}
+		python $__tool_directory__/scripts/S01_concatenate.py ${zip}
 
 		#if $format.format_run == "nucleic" :
 			nucleic $format.zip_nuc

galaxy_wrappers/06_ConcatPhyl/scripts

@@ -0,0 +1 @@
+../../scripts/06_ConcatPhyl

scripts/script_to_choose.py → scripts/01_Filter_Assemblies/S01_script_to_choose.py

@@ -29,20 +29,20 @@
         suffix=name[:2]
         #if re.match(fas, name) :
     #os.system("python /w/galaxy/galaxy4misharl/galaxy-dist/tools/abims/julie/oasearch/filter_assembly/remove_redondancy_from_oases_output_v3.1.py %s %s" %(name2, name3))
-        os.system("python %s/remove_redondancy_from_oases_output_v3.1.py %s %s" %(script_path,name2, name3))
+        os.system("python %s/S02a_remove_redondancy_from_velvet_oases.py %s %s" %(script_path,name2, name3))
         #elif re.match(fasta, name) :
         os.system("sed -e 's/Locus_/%s/g' -e 's/_Confidence_/_/g' -e 's/_Transcript_/_/g' -e 's/_Length_/_/g' %s > %s" % (suffix,name3,name4))
         #os.system("python /w/galaxy/galaxy4misharl/galaxy-dist/tools/abims/julie/oasearch/filter_assembly/remove_redondancy_from_oases_output_v3.0.py %s %s" %(name, name2))
         #Pierre guillaume find_orf script for keeping the longuest ORF
-        os.system("python %s/find_orf.py %s %s" %(script_path,name4,name5))
+        os.system("python %s/S04_find_orf.py %s %s" %(script_path,name4,name5))
 
 	#Apply cap3
         os.system("cap3  %s -p %s -o %s"%(name5,sys.argv[4],sys.argv[5]))
         #Fasta sequences on one line
         #Il faudrait faire un merge des singlets et contigs! TODO
         os.system("zcat -f < '%s.cap.singlets' | fasta_formatter -w 0 -o '%s'" % (name5,name6))
         #Apply pgbrun script filter script TODO length parameter
-        os.system("python %s/filter.py %s %s %s" %(script_path,name6,sys.argv[3],name7))  
+        os.system("python %s/S05_filter.py %s %s %s" %(script_path,name6,sys.argv[3],name7))  
         L1.append(name7)
     f = zipfile.ZipFile("sequences_filtered.zip", "w")
     for files in L1 :
@@ -66,18 +66,18 @@
         #replace white space by "_" 
         os.system("sed -e 's/ /_/g' %s > %s " % (name2,name3))
         #Format the name of the sequences with good name
-        os.system("python %s/02_format_fasta_name_TRINITY.py %s %s %s" %(script_path,name3, name4,suffix))
+        os.system("python %s/S02b_format_fasta_name_trinity.py %s %s %s" %(script_path,name3, name4,suffix))
         #Apply first script to avoid reductant sequences
-        os.system("python %s/01_Choose_One_variants_per_locus_TRINITY_v1.0.py %s %s" %(script_path,name4, name5))
+        os.system("python %s/S03_choose_one_variants_per_locus_trinity.py %s %s" %(script_path,name4, name5))
     #Pierre guillaume find_orf script for keeping the longuest ORF
-        os.system("python %s/find_orf.py %s %s" %(script_path,name5,name6))
+        os.system("python %s/S04_find_orf.py %s %s" %(script_path,name5,name6))
         #Apply cap3
         os.system("cap3  %s -p %s -o %s"%(name6,sys.argv[4],sys.argv[5]))
         #Fasta sequences on one line
         #Il faudrait faire un merge des singlets et contigs! TODO
         os.system("zcat -f < '%s.cap.singlets' | fasta_formatter -w 0 -o '%s'" % (name6,name7))
         #Apply pgbrun script filter script TODO length parameter
-        os.system("python %s/filter.py %s %s %s" %(script_path,name7,sys.argv[3],name8)) 
+        os.system("python %s/S05_filter.py %s %s %s" %(script_path,name7,sys.argv[3],name8)) 
         L1.append(name8)
     f = zipfile.ZipFile("sequences_filtered.zip", "w")
     for files in L1 :