Mercurial > repos > abims-sbr > concatphyl
changeset 9:ff1a3a790363 draft
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit f1ba8d136e0129f3e8435b25a95f70f697d51464-dirty
author | abims-sbr |
---|---|
date | Tue, 03 Jul 2018 10:55:20 -0400 |
parents | ad3446d7f794 |
children | 5cae58aa1181 |
files | ConcatPhyl.xml scripts/S01_concatenate.py static/images/adaptsearch_picture_helps.png test-data/input_from_CDS_Search/locus147_sp3_sp3.fasta test-data/input_from_CDS_Search/locus17_sp3_sp3.fasta test-data/input_from_CDS_Search/locus183_sp3_sp3.fasta test-data/input_from_CDS_Search/locus334_sp3_sp3.fasta test-data/input_from_CDS_Search/orthogroup_147_sp3_sp3.fasta test-data/input_from_CDS_Search/orthogroup_17_sp3_sp3.fasta test-data/input_from_CDS_Search/orthogroup_183_sp3_sp3.fasta test-data/input_from_CDS_Search/orthogroup_334_sp3_sp3.fasta |
diffstat | 11 files changed, 43 insertions(+), 36 deletions(-) [+] |
line wrap: on
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--- 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" />
--- 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
--- 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
--- 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
--- 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
--- 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
--- /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
--- /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
--- /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
--- /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