| Previous changeset 53:080fd5739bb4 (2018-03-20) Next changeset 55:b0b62dcd0a35 (2018-09-18) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 62a9135bf04aec398d3172d17ccd60f5242d8e82 |
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modified:
FPKM_count.xml RNA_fragment_size.xml RPKM_saturation.xml geneBody_coverage.xml geneBody_coverage2.xml infer_experiment.xml inner_distance.xml junction_annotation.xml junction_saturation.xml read_distribution.xml rseqc_macros.xml tin.xml |
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removed:
test-data/output.RNA_fragment_size.txt test-data/output.tin.summary.txt |
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| diff -r 080fd5739bb4 -r 5873cd7afb67 FPKM_count.xml --- a/FPKM_count.xml Tue Mar 20 05:37:48 2018 -0400 +++ b/FPKM_count.xml Wed Jun 13 18:02:25 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="rseqc_FPKM_count" name="FPKM Count" version="@WRAPPER_VERSION@"> +<tool id="rseqc_FPKM_count" name="FPKM Count" version="@WRAPPER_VERSION@.1"> <description>calculates raw read count, FPM, and FPKM for each gene</description> <macros> |
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| diff -r 080fd5739bb4 -r 5873cd7afb67 RNA_fragment_size.xml --- a/RNA_fragment_size.xml Tue Mar 20 05:37:48 2018 -0400 +++ b/RNA_fragment_size.xml Wed Jun 13 18:02:25 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="rseqc_RNA_fragment_size" name="RNA fragment size" version="@WRAPPER_VERSION@"> +<tool id="rseqc_RNA_fragment_size" name="RNA fragment size" version="@WRAPPER_VERSION@.1"> <description> calculates the fragment size for each gene/transcript </description> @@ -35,7 +35,18 @@ <test> <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" /> <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" /> - <output name="output" file="output.RNA_fragment_size.txt" /> + <output name="output"> + <assert_contents> + <has_line_matching expression="^chrom\ttx_start\ttx_end\tsymbol\tfrag_count\tfrag_mean\tfrag_median\tfrag_std$" /> + <has_line_matching expression="^chr1\t11873\t14409\tNR_046018\t1\t0\t0\t0$" /> + <has_line_matching expression="^chr1\t14361\t29370\tNR_024540\t14\t66.5\t51.0\t41.119599080\d+$" /> + <has_line_matching expression="^chr1\t17368\t17436\tNR_106918\t0\t0\t0\t0$" /> + <has_line_matching expression="^chr1\t17368\t17436\tNR_107062\t0\t0\t0\t0$" /> + <has_line_matching expression="^chr1\t34610\t36081\tNR_026818\t0\t0\t0\t0$" /> + <has_line_matching expression="^chr1\t34610\t36081\tNR_026820\t0\t0\t0\t0$" /> + <has_line_matching expression="^chr1\t69090\t70008\tNM_001005484\t0\t0\t0\t0$" /> + </assert_contents> + </output> </test> </tests> |
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| diff -r 080fd5739bb4 -r 5873cd7afb67 RPKM_saturation.xml --- a/RPKM_saturation.xml Tue Mar 20 05:37:48 2018 -0400 +++ b/RPKM_saturation.xml Wed Jun 13 18:02:25 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="rseqc_RPKM_saturation" name="RPKM Saturation" version="@WRAPPER_VERSION@"> +<tool id="rseqc_RPKM_saturation" name="RPKM Saturation" version="@WRAPPER_VERSION@.1"> <description>calculates raw count and RPKM values for transcript at exon, intron, and mRNA level</description> <macros> |
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| diff -r 080fd5739bb4 -r 5873cd7afb67 geneBody_coverage.xml --- a/geneBody_coverage.xml Tue Mar 20 05:37:48 2018 -0400 +++ b/geneBody_coverage.xml Wed Jun 13 18:02:25 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="rseqc_geneBody_coverage" name="Gene Body Converage (BAM)" version="@WRAPPER_VERSION@.1"> +<tool id="rseqc_geneBody_coverage" name="Gene Body Converage (BAM)" version="@WRAPPER_VERSION@.2"> <description> Read coverage over gene body. </description> |
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| diff -r 080fd5739bb4 -r 5873cd7afb67 geneBody_coverage2.xml --- a/geneBody_coverage2.xml Tue Mar 20 05:37:48 2018 -0400 +++ b/geneBody_coverage2.xml Wed Jun 13 18:02:25 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="rseqc_geneBody_coverage2" name="Gene Body Converage (Bigwig)" version="@WRAPPER_VERSION@"> +<tool id="rseqc_geneBody_coverage2" name="Gene Body Converage (Bigwig)" version="@WRAPPER_VERSION@.1"> <description> Read coverage over gene body </description> |
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| diff -r 080fd5739bb4 -r 5873cd7afb67 infer_experiment.xml --- a/infer_experiment.xml Tue Mar 20 05:37:48 2018 -0400 +++ b/infer_experiment.xml Wed Jun 13 18:02:25 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="rseqc_infer_experiment" name="Infer Experiment" version="@WRAPPER_VERSION@"> +<tool id="rseqc_infer_experiment" name="Infer Experiment" version="@WRAPPER_VERSION@.1"> <description>speculates how RNA-seq were configured</description> <macros> |
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| diff -r 080fd5739bb4 -r 5873cd7afb67 inner_distance.xml --- a/inner_distance.xml Tue Mar 20 05:37:48 2018 -0400 +++ b/inner_distance.xml Wed Jun 13 18:02:25 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="rseqc_inner_distance" name="Inner Distance" version="@WRAPPER_VERSION@"> +<tool id="rseqc_inner_distance" name="Inner Distance" version="@WRAPPER_VERSION@.1"> <description>calculate the inner distance (or insert size) between two paired RNA reads</description> <macros> |
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| diff -r 080fd5739bb4 -r 5873cd7afb67 junction_annotation.xml --- a/junction_annotation.xml Tue Mar 20 05:37:48 2018 -0400 +++ b/junction_annotation.xml Wed Jun 13 18:02:25 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="rseqc_junction_annotation" name="Junction Annotation" version="@WRAPPER_VERSION@"> +<tool id="rseqc_junction_annotation" name="Junction Annotation" version="@WRAPPER_VERSION@.1"> <description>compares detected splice junctions to reference gene model</description> <macros> |
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| diff -r 080fd5739bb4 -r 5873cd7afb67 junction_saturation.xml --- a/junction_saturation.xml Tue Mar 20 05:37:48 2018 -0400 +++ b/junction_saturation.xml Wed Jun 13 18:02:25 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="rseqc_junction_saturation" name="Junction Saturation" version="@WRAPPER_VERSION@"> +<tool id="rseqc_junction_saturation" name="Junction Saturation" version="@WRAPPER_VERSION@.1"> <description>detects splice junctions from each subset and compares them to reference gene model</description> <macros> |
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| diff -r 080fd5739bb4 -r 5873cd7afb67 read_distribution.xml --- a/read_distribution.xml Tue Mar 20 05:37:48 2018 -0400 +++ b/read_distribution.xml Wed Jun 13 18:02:25 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="rseqc_read_distribution" name="Read Distribution" version="@WRAPPER_VERSION@"> +<tool id="rseqc_read_distribution" name="Read Distribution" version="@WRAPPER_VERSION@.1"> <description>calculates how mapped reads were distributed over genome feature</description> <macros> |
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| diff -r 080fd5739bb4 -r 5873cd7afb67 rseqc_macros.xml --- a/rseqc_macros.xml Tue Mar 20 05:37:48 2018 -0400 +++ b/rseqc_macros.xml Wed Jun 13 18:02:25 2018 -0400 |
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| @@ -26,7 +26,7 @@ </xml> <xml name="refgene_param"> - <param name="refgene" type="data" format="bed" label="Reference gene model" help="(--refgene)"/> + <param name="refgene" type="data" format="bed12" label="Reference gene model" help="(--refgene)"/> </xml> <xml name="mapq_param"> |
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| diff -r 080fd5739bb4 -r 5873cd7afb67 test-data/output.RNA_fragment_size.txt --- a/test-data/output.RNA_fragment_size.txt Tue Mar 20 05:37:48 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,8 +0,0 @@ -chrom tx_start tx_end symbol frag_count frag_mean frag_median frag_std -chr1 11873 14409 NR_046018 1 0 0 0 -chr1 14361 29370 NR_024540 14 66.5 51.0 41.119599080869314 -chr1 17368 17436 NR_106918 0 0 0 0 -chr1 17368 17436 NR_107062 0 0 0 0 -chr1 34610 36081 NR_026818 0 0 0 0 -chr1 34610 36081 NR_026820 0 0 0 0 -chr1 69090 70008 NM_001005484 0 0 0 0 |
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| diff -r 080fd5739bb4 -r 5873cd7afb67 test-data/output.tin.summary.txt --- a/test-data/output.tin.summary.txt Tue Mar 20 05:37:48 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,2 +0,0 @@ -Bam_file TIN(mean) TIN(median) TIN(stdev) -input.bam 8.870967741935486 8.870967741935486 0.0 |
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| diff -r 080fd5739bb4 -r 5873cd7afb67 tin.xml --- a/tin.xml Tue Mar 20 05:37:48 2018 -0400 +++ b/tin.xml Wed Jun 13 18:02:25 2018 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="rseqc_tin" name="Transcript Integrity Number" version="@WRAPPER_VERSION@"> +<tool id="rseqc_tin" name="Transcript Integrity Number" version="@WRAPPER_VERSION@.1"> <description> evaluates RNA integrity at a transcript level </description> @@ -50,7 +50,12 @@ <test> <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/> <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed"/> - <output name="outputsummary" file="output.tin.summary.txt"/> + <output name="outputsummary"> + <assert_contents> + <has_line_matching expression="^Bam_file\tTIN\(mean\)\tTIN\(median\)\tTIN\(stdev\)$" /> + <has_line_matching expression="^input\.bam\t8\.8709677419\d+\t8\.8709677419\d+\t0\.0$" /> + </assert_contents> + </output> <output name="outputxls" file="output.tin.xls"/> </test> </tests> |