Mercurial > repos > abims-sbr > mutcount
diff MutCount.xml @ 9:04a9ada73cc4 draft
planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit f1ba8d136e0129f3e8435b25a95f70f697d51464-dirty
| author | abims-sbr |
|---|---|
| date | Tue, 03 Jul 2018 10:55:46 -0400 |
| parents | 705a7bf4c311 |
| children | f62c76aab669 |
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--- a/MutCount.xml Fri Mar 16 05:11:04 2018 -0400 +++ b/MutCount.xml Tue Jul 03 10:55:46 2018 -0400 @@ -25,21 +25,19 @@ #end if #if str($method.method_run) == "separated" : - #set $infiles = "" #for $input in $method.sep_file ln -s '$input' '$input.element_identifier'; - #set $infiles = $infiles + $input.element_identifier + "," + echo '$input.element_identifier' >> list_files; #end for - #set $infiles = $infiles[:-1] #if str($method.format_run)== "nucleic" : - python '$__tool_directory__/scripts/S02b_study_seq_composition_nuc.py' '$infiles' ${method.concat_phy} + python '$__tool_directory__/scripts/S02b_study_seq_composition_nuc.py' ${method.concat_phy} list_files #end if #if str($method.format_run)== "proteic" : cp '$__tool_directory__/scripts/amino_acid_properties.csv' . && - python '$__tool_directory__/scripts/S01b_study_seq_composition_aa.py' '$infiles' ${method.concat_phy} + python '$__tool_directory__/scripts/S01b_study_seq_composition_aa.py' ${method.concat_phy} list_files #end if #end if @@ -157,7 +155,6 @@ </outputs> <tests> - <test> <conditional name="method" > <param name="method_run" value="concat" /> @@ -176,32 +173,31 @@ <output name="aa_transitions_freqs" value="OUT_concat/aa_transitions_freqs.csv" lines_diff="72"/> <output name="aatypes_transitions_freqs" value="OUT_concat/aatypes_transitions_freqs.csv" lines_diff="72"/> </test> - <test> <conditional name="method" > <param name="method_run" value="separated" /> <param name="format_run" value="nucleic" /> - <param name="sep_file" ftype="fasta" value="sep_nuc/locus1_sp6_sp6.fasta,sep_nuc/locus1_sp8_sp8.fasta,sep_nuc/locus2_sp6_sp6.fasta" /> + <param name="sep_file" ftype="fasta" value="sep_nuc/orthogroup_1_sp6_sp6.fasta,sep_nuc/orthogroup_1_sp8_sp8.fasta,sep_nuc/orthogroup_2_sp6_sp6.fasta" /> <param name="concat_phy" ftype="fasta" value="phylogeny_concat.fasta" /> </conditional> <output name="nuc_comp"> <assert_contents> - <has_line line="locus2_sp6_sp6.fasta,0.30208,0.23958,0.19792,0.26042,0.29688,0.27604,0.18229,0.24479,NA,NA,NA,NA,0.30208,0.24479,0.19792,0.25521,NA,NA,NA,NA,0.31250,0.26042,0.17188,0.25521,0.32292,0.21875,0.20312,0.25521,NA,NA,NA,NA,NA,NA,NA,NA,0.31771,0.25521,0.17708,0.25000"/> + <has_line line="orthogroup_2_sp6_sp6.fasta,0.30208,0.23958,0.19792,0.26042,0.29688,0.27604,0.18229,0.24479,NA,NA,NA,NA,0.30208,0.24479,0.19792,0.25521,NA,NA,NA,NA,0.31250,0.26042,0.17188,0.25521,0.32292,0.21875,0.20312,0.25521,NA,NA,NA,NA,NA,NA,NA,NA,0.31771,0.25521,0.17708,0.25000"/> </assert_contents> </output> <output name="percent_gc"> <assert_contents> - <has_line line="locus2_sp6_sp6.fasta,45.83333,42.70833,NA,45.31250,NA,42.70833,45.83333,NA,NA,42.70833" /> + <has_line line="orthogroup_2_sp6_sp6.fasta,45.83333,42.70833,NA,45.31250,NA,42.70833,45.83333,NA,NA,42.70833" /> </assert_contents> </output> <output name="percent_pur"> <assert_contents> - <has_line line="locus2_sp6_sp6.fasta,56.25000,54.16667,NA,55.72917,NA,56.77083,57.81250,NA,NA,56.77083" /> + <has_line line="orthogroup_2_sp6_sp6.fasta,56.25000,54.16667,NA,55.72917,NA,56.77083,57.81250,NA,NA,56.77083" /> </assert_contents> </output> <output name="purine_load"> <assert_contents> - <has_line line="locus2_sp6_sp6.fasta,192,12,12,62.50000,62.50000,192,12,4,62.50000,20.83333,NA,NA,NA,NA,NA,192,11,11,57.29167,57.29167,NA,NA,NA,NA,NA,192,16,10,83.33333,52.08333,192,10,20,52.08333,104.16667,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,192,14,12,72.91667,62.50000" /> + <has_line line="orthogroup_2_sp6_sp6.fasta,192,12,12,62.50000,62.50000,192,12,4,62.50000,20.83333,NA,NA,NA,NA,NA,192,11,11,57.29167,57.29167,NA,NA,NA,NA,NA,192,16,10,83.33333,52.08333,192,10,20,52.08333,104.16667,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,192,14,12,72.91667,62.50000" /> </assert_contents> </output> </test> @@ -210,30 +206,31 @@ <conditional name="method" > <param name="method_run" value="separated" /> <param name="format_run" value="proteic" /> - <param name="sep_file" ftype="fasta" value="sep_aa/locus1_sp6_sp6.fasta,sep_aa/locus1_sp8_sp8.fasta,sep_aa/locus2_sp6_sp6.fasta" /> + <param name="sep_file" ftype="fasta" value="sep_aa/orthogroup_1_sp6_sp6.fasta,sep_aa/orthogroup_1_sp8_sp8.fasta,sep_aa/orthogroup_2_sp6_sp6.fasta" /> <param name="concat_phy" ftype="fasta" value="phylogeny_concat.fasta" /> </conditional> <output name="ivywrel"> <assert_contents> - <has_line line="locus1_sp8_sp8.fasta,25.00000,0.36765,28.00000,0.36364,NA,NA,NA,NA,27.00000,0.35065,27.00000,0.35065,28.00000,0.36364,0.00000,0.00000,27.00000,0.40909,27.00000,0.35065" /> + <has_line line="orthogroup_1_sp8_sp8.fasta,25.00000,0.36765,28.00000,0.36364,NA,NA,NA,NA,27.00000,0.35065,27.00000,0.35065,28.00000,0.36364,0.00000,0.00000,27.00000,0.40909,27.00000,0.35065" /> </assert_contents> </output> <output name="rhkde"> <assert_contents> - <has_line line="locus1_sp6_sp6.fasta,28.00000,0.35897,14.00000,0.17949,14.00000,0.17949,30.00000,0.38462,16.00000,0.20513,14.00000,0.17949,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,30.00000,0.38462,16.00000,0.20513,14.00000,0.17949,30.00000,0.38462,16.00000,0.20513,14.00000,0.17949,30.00000,0.38462,16.00000,0.20513,14.00000,0.17949,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,30.00000,0.38462,16.00000,0.20513,14.00000,0.17949"/> + <has_line line="orthogroup_1_sp6_sp6.fasta,28.00000,0.35897,14.00000,0.17949,14.00000,0.17949,30.00000,0.38462,16.00000,0.20513,14.00000,0.17949,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,30.00000,0.38462,16.00000,0.20513,14.00000,0.17949,30.00000,0.38462,16.00000,0.20513,14.00000,0.17949,30.00000,0.38462,16.00000,0.20513,14.00000,0.17949,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,30.00000,0.38462,16.00000,0.20513,14.00000,0.17949"/> </assert_contents> </output> <output name="payre_mvgds"> <assert_contents> - <has_line line="locus1_sp8_sp8.fasta,16.00000,0.23529,3.00000,0.04412,27.00000,0.39706,0.59259,0.11111,18.00000,0.23377,4.00000,0.05195,29.00000,0.37662,0.62069,0.13793,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,19.00000,0.24675,6.00000,0.07792,30.00000,0.38961,0.63333,0.20000,20.00000,0.25974,7.00000,0.09091,32.00000,0.41558,0.62500,0.21875,20.00000,0.25974,5.00000,0.06494,29.00000,0.37662,0.68966,0.17241,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,14.00000,0.21212,2.00000,0.03030,26.00000,0.39394,0.53846,0.07692,19.00000,0.24675,6.00000,0.07792,32.00000,0.41558,0.59375,0.18750"/> + <has_line line="orthogroup_1_sp8_sp8.fasta,16.00000,0.23529,3.00000,0.04412,27.00000,0.39706,0.59259,0.11111,18.00000,0.23377,4.00000,0.05195,29.00000,0.37662,0.62069,0.13793,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,19.00000,0.24675,6.00000,0.07792,30.00000,0.38961,0.63333,0.20000,20.00000,0.25974,7.00000,0.09091,32.00000,0.41558,0.62500,0.21875,20.00000,0.25974,5.00000,0.06494,29.00000,0.37662,0.68966,0.17241,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,14.00000,0.21212,2.00000,0.03030,26.00000,0.39394,0.53846,0.07692,19.00000,0.24675,6.00000,0.07792,32.00000,0.41558,0.59375,0.18750"/> </assert_contents> </output> <output name="avlimfyw"> <assert_contents> - <has_line line="locus2_sp6_sp6.fasta,27.00000,0.42188,21.00000,0.32812,6.00000,0.09375,28.00000,0.43750,22.00000,0.34375,6.00000,0.09375,NA,NA,NA,NA,NA,NA,28.00000,0.43750,22.00000,0.34375,6.00000,0.09375,NA,NA,NA,NA,NA,NA,28.00000,0.43750,22.00000,0.34375,6.00000,0.09375,30.00000,0.46875,24.00000,0.37500,6.00000,0.09375,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,28.00000,0.43750,22.00000,0.34375,6.00000,0.09375"/> + <has_line line="orthogroup_2_sp6_sp6.fasta,27.00000,0.42188,21.00000,0.32812,6.00000,0.09375,28.00000,0.43750,22.00000,0.34375,6.00000,0.09375,NA,NA,NA,NA,NA,NA,28.00000,0.43750,22.00000,0.34375,6.00000,0.09375,NA,NA,NA,NA,NA,NA,28.00000,0.43750,22.00000,0.34375,6.00000,0.09375,30.00000,0.46875,24.00000,0.37500,6.00000,0.09375,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,28.00000,0.43750,22.00000,0.34375,6.00000,0.09375"/> </assert_contents> </output> </test> + </tests> <help>