# HG changeset patch # User iuc # Date 1510244252 18000 # Node ID 76d290331481c8c0d9d39c1903b4d619add2fa06 # Parent 6e45b443ef1fe3ae4e95100b8199b8ee464c6a69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 diff -r 6e45b443ef1f -r 76d290331481 macros.xml --- a/macros.xml Thu Jun 01 12:16:04 2017 -0400 +++ b/macros.xml Thu Nov 09 11:17:32 2017 -0500 @@ -2,6 +2,7 @@ stringtie + samtools diff -r 6e45b443ef1f -r 76d290331481 stringtie.xml --- a/stringtie.xml Thu Jun 01 12:16:04 2017 -0400 +++ b/stringtie.xml Thu Nov 09 11:17:32 2017 -0500 @@ -1,4 +1,4 @@ - + transcript assembly and quantification macros.xml @@ -7,133 +7,183 @@ /dev/null + && + sed -i.bak 's/,/\t/g' '$legend' && - prepDE.py - -i ./special_de_output/ - -g gene_cout_matrix.tsv - -t transcripts_count_matrix.tsv - -l $guide.special_outputs.read_length - #if str($option_set.options) == 'advanced': - -s '$option_set.name_prefix' - #end if - #if $guide.special_outputs.clustering: - -c - --legend ./legend.tsv + sed -i.bak 's/\r//g' '$legend' + #end if + + > /dev/null - && - sed -i.bak 's/,/\t/g' ./legend.tsv - - #end if - && - sed -i.bak 's/,/\t/g' transcripts_count_matrix.tsv - && - sed -i.bak 's/,/\t/g' gene_cout_matrix.tsv - #end if - #end if + && + sed -i.bak 's/,/\t/g' '$transcript_counts' + && + sed -i.bak 's/\r//g' '$transcript_counts' + && + sed -i.bak 's/,/\t/g' '$gene_counts' + && + sed -i.bak 's/\r//g' '$gene_counts' + #end if +#end if ]]> - + + + + + + - - - + + + - - + + + + + + + + + + + + + + + + + + - + - - + + - - + + + + + + + + + + + + + - - - - +
+ + + + + + - - - - - - - - - - - - - - - - - + + + + + + + + + +
- option_set['options'] == 'advanced' and option_set['abundance_estimation'] + adv['abundance_estimation'] - - guide['use_guide'] == 'yes' + + guide['use_guide'] == 'yes' and guide['coverage_file'] is True @@ -155,105 +205,273 @@ label="${tool.name} on ${on_string}: intron to transcript mapping"> guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'ballgown' - + guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'deseq2' - + guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'deseq2' - + guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'deseq2' and guide['special_outputs']['clustering'] is True - + + - - - + + - - - - - - - - - - - + + - - - + + + + + + + + + + - + + + + - - + - + - + + - - + + + - + - + - + + - - + + - + + - - - + + - + + + + + + + + -
+
\ No newline at end of file diff -r 6e45b443ef1f -r 76d290331481 test-data/cached_locally/gene_sets.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/gene_sets.loc Thu Nov 09 11:17:32 2017 -0500 @@ -0,0 +1,1 @@ +hg38 hg38 hg38GTF ${__HERE__}/ref.gtf diff -r 6e45b443ef1f -r 76d290331481 test-data/cached_locally/ref.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/ref.gtf Thu Nov 09 11:17:32 2017 -0500 @@ -0,0 +1,4 @@ +test_chromosome Cufflinks transcript 53 550 1000 + . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; FPKM "10679134.4063403048"; frac "1.000000"; conf_lo "8542701.791788"; conf_hi "12815567.020892"; cov "145.770185"; +test_chromosome Cufflinks exon 53 250 1000 + . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "1"; FPKM "10679134.4063403048"; frac "1.000000"; conf_lo "8542701.791788"; conf_hi "12815567.020892"; cov "145.770185"; +test_chromosome Cufflinks exon 351 400 1000 + . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "2"; FPKM "10679134.4063403048"; frac "1.000000"; conf_lo "8542701.791788"; conf_hi "12815567.020892"; cov "145.770185"; +test_chromosome Cufflinks exon 501 550 1000 + . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "3"; FPKM "10679134.4063403048"; frac "1.000000"; conf_lo "8542701.791788"; conf_hi "12815567.020892"; cov "145.770185"; diff -r 6e45b443ef1f -r 76d290331481 test-data/deseq2/gene_counts.tsv --- a/test-data/deseq2/gene_counts.tsv Thu Jun 01 12:16:04 2017 -0400 +++ b/test-data/deseq2/gene_counts.tsv Thu Nov 09 11:17:32 2017 -0500 @@ -1,2 +1,2 @@ - sample1 -CUFF.1 574 +gene_id sample1 +CUFF.1 182 diff -r 6e45b443ef1f -r 76d290331481 test-data/deseq2/transcript_counts.tsv --- a/test-data/deseq2/transcript_counts.tsv Thu Jun 01 12:16:04 2017 -0400 +++ b/test-data/deseq2/transcript_counts.tsv Thu Nov 09 11:17:32 2017 -0500 @@ -1,2 +1,2 @@ - sample1 -CUFF.1.1 574 +transcript_id sample1 +CUFF.1.1 182 diff -r 6e45b443ef1f -r 76d290331481 test-data/stringtie_out6.gtf --- a/test-data/stringtie_out6.gtf Thu Jun 01 12:16:04 2017 -0400 +++ b/test-data/stringtie_out6.gtf Thu Nov 09 11:17:32 2017 -0500 @@ -1,4 +1,4 @@ -# stringtie /tmp/tmpJfKWNy/files/000/dataset_22.dat -o /tmp/tmpJfKWNy/files/000/dataset_24.dat -p 1 -C /tmp/tmpJfKWNy/files/000/dataset_25.dat -G /tmp/tmpJfKWNy/files/000/dataset_23.dat -e -b ./special_de_output/sample1/ +# stringtie /tmp/tmpSoPTYX/files/000/dataset_1.dat -o /tmp/tmpSoPTYX/files/000/dataset_3.dat -p 1 -G guide.gff -C /tmp/tmpSoPTYX/files/000/dataset_4.dat -e -b ./special_de_output/sample1/ -f 0.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95 # StringTie version 1.3.3 test_chromosome StringTie transcript 53 550 1000 + . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; cov "45.795296"; FPKM "3354966.750000"; TPM "1000000.000000"; test_chromosome StringTie exon 53 250 1000 + . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "1"; cov "49.777779"; diff -r 6e45b443ef1f -r 76d290331481 tool-data/gene_sets.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/gene_sets.loc.sample Thu Nov 09 11:17:32 2017 -0500 @@ -0,0 +1,14 @@ +# This is a sample file distributed with featureCounts that enables it and other# tools to use gene/exon annotations in the GFF/GTF format. +# +# The gene_sets.loc file syntax is: +# +# +# Please ensure that the above fields are tab separated. +# +# In case you have TWO or MORE providers PER dbkey, the one mentioned +# first in the file, should have the "default" priority. +# +#Example: +# +#Homo_sapiens.GRCh37.74 hg19 GRCh37 (hg19) annotation from Ensembl, release 74 /depot/data2/galaxy/hg19/gene_sets/Homo_sapiens.GRCh37.74.gtf +#Homo_sapiens.NCBI36.54 hg18 hg18 annotation from Ensembl, release 54 /depot/data2/galaxy/hg18/gene_sets/Homo_sapiens.NCBI36.54.gtf diff -r 6e45b443ef1f -r 76d290331481 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Thu Nov 09 11:17:32 2017 -0500 @@ -0,0 +1,7 @@ + + + + value, dbkey, name, path + +
+
diff -r 6e45b443ef1f -r 76d290331481 tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Thu Nov 09 11:17:32 2017 -0500 @@ -0,0 +1,6 @@ + + + value, dbkey, name, path + +
+