| Previous changeset 3:48b891c1c2aa (2015-05-14) Next changeset 5:f504b3b7e49d (2015-10-21) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit ba7b53894c61fea9a93550f865e9ed2753a904cf |
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modified:
stringtie.xml test-data/ballgown/e_data.ctab tool_dependencies.xml |
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| diff -r 48b891c1c2aa -r df42808cc33a stringtie.xml --- a/stringtie.xml Thu May 14 12:36:35 2015 -0400 +++ b/stringtie.xml Wed Aug 12 07:07:40 2015 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="stringtie" name="StringTie" version="1.0.3"> +<tool id="stringtie" name="StringTie" version="1.0.4"> <description>transcript assembly and quantification</description> <requirements> - <requirement type="package" version="1.0.3">stringtie</requirement> + <requirement type="package" version="1.0.4">stringtie</requirement> </requirements> <command><![CDATA[ stringtie "$input_bam" @@ -21,7 +21,7 @@ -j "$option_set.min_anchor_cov" -c "$option_set.min_bundle_cov" -s "$option_set.maxcov" - -g "$option_set.bdist" + -g "$option_set.bdist" -M "$option_set.bundle_fraction" $option_set.sensitive $option_set.disable_trimming #end if ]]> @@ -87,21 +87,21 @@ <param ftype="bam" name="input_bam" value="stringtie_in1.bam" /> <param name="use_guide" value="no" /> <param name="options" value="default" /> - <output file="stringtie_out1.gtf" ftype="gtf" name="output_gtf" /> + <output file="stringtie_out1.gtf" ftype="gtf" name="output_gtf" lines_diff="2" /> </test> <test> <param ftype="bam" name="input_bam" value="stringtie_in1.bam" /> <param name="use_guide" value="no" /> <param name="options" value="advanced" /> <param name="fraction" value="0.17" /> - <output file="stringtie_out2.gtf" ftype="gtf" name="output_gtf" /> + <output file="stringtie_out2.gtf" ftype="gtf" name="output_gtf" lines_diff="2" /> </test> <test> <param ftype="bam" name="input_bam" value="stringtie_in1.bam" /> <param name="use_guide" value="yes" /> <param name="guide_gff" value="stringtie_in.gtf" /> <param name="options" value="default" /> - <output file="stringtie_out3.gtf" ftype="gtf" name="output_gtf" /> + <output file="stringtie_out3.gtf" ftype="gtf" name="output_gtf" lines_diff="2" /> </test> <test> <param ftype="bam" name="input_bam" value="stringtie_in1.bam" /> @@ -109,7 +109,7 @@ <param name="guide_gff" value="stringtie_in.gtf" /> <param name="options" value="advanced" /> <param name="fraction" value="0.17" /> - <output file="stringtie_out4.gtf" ftype="gtf" name="output_gtf" /> + <output file="stringtie_out4.gtf" ftype="gtf" name="output_gtf" lines_diff="2" /> </test> <test> <param ftype="bam" name="input_bam" value="stringtie_in1.bam" /> @@ -122,7 +122,7 @@ <output file="ballgown/t_data.ctab" ftype="tabular" name="transcript_expression" /> <output file="ballgown/e2t.ctab" ftype="tabular" name="exon_transcript_mapping" /> <output file="ballgown/i2t.ctab" ftype="tabular" name="intron_transcript_mapping" /> - <output file="stringtie_out5.gtf" ftype="gtf" name="output_gtf" /> + <output file="stringtie_out5.gtf" ftype="gtf" name="output_gtf" lines_diff="2" /> <output file="stringtie_out_coverage.gtf" ftype="gff3" name="coverage" /> </test> </tests> |
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| diff -r 48b891c1c2aa -r df42808cc33a test-data/ballgown/e_data.ctab --- a/test-data/ballgown/e_data.ctab Thu May 14 12:36:35 2015 -0400 +++ b/test-data/ballgown/e_data.ctab Wed Aug 12 07:07:40 2015 -0400 |
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| @@ -1,4 +1,4 @@ e_id chr strand start end rcount ucount mrcount cov cov_sd mcov mcov_sd -1 test_chromosome + 53 250 154 154 154.00 49.7778 22.0747 49.7778 22.0747 +1 test_chromosome + 53 250 158 158 158.00 49.7778 22.0747 49.7778 22.0747 2 test_chromosome + 351 400 73 73 73.00 54.1600 6.1753 54.1600 6.1753 3 test_chromosome + 501 550 38 38 38.00 21.6400 12.4350 21.6400 12.4350 |
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| diff -r 48b891c1c2aa -r df42808cc33a tool_dependencies.xml --- a/tool_dependencies.xml Thu May 14 12:36:35 2015 -0400 +++ b/tool_dependencies.xml Wed Aug 12 07:07:40 2015 -0400 |
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| @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> - <package name="stringtie" version="1.0.3"> - <repository changeset_revision="76595a6609c0" name="package_stringtie_1_0_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + <package name="stringtie" version="1.0.4"> + <repository changeset_revision="f3818f4bc127" name="package_stringtie_1_0_4" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency> |