Mercurial > repos > nilesh > rseqc
changeset 62:473382134e56 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit ccb6f7edba5492f4750ef8a59c4f91eb67fdbbec
| author | iuc |
|---|---|
| date | Wed, 22 Feb 2023 15:06:01 +0000 |
| parents | 5968573462fa |
| children | 27e16a30667a |
| files | FPKM_count.xml RPKM_saturation.xml clipping_profile.xml deletion_profile.xml insertion_profile.xml junction_annotation.xml mismatch_profile.xml read_GC.xml read_NVC.xml read_duplication.xml rseqc_macros.xml test-data/output.FPKM.xls test-data/output01.tab test-data/output02.tab tin.xml |
| diffstat | 15 files changed, 48 insertions(+), 32 deletions(-) [+] |
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--- a/FPKM_count.xml Sat Dec 10 11:23:05 2022 +0000 +++ b/FPKM_count.xml Wed Feb 22 15:06:01 2023 +0000 @@ -15,7 +15,6 @@ <command><![CDATA[ @BAM_SAM_INPUTS@ FPKM_count.py -i 'input.${extension}' -o output -r '${refgene}' - #if str($strand_type.strand_specific) == "pair" -d #if str($strand_type.pair_type) == "sd" @@ -24,7 +23,6 @@ '1+-,1-+,2++,2--' #end if #end if - #if str($strand_type.strand_specific) == "single" -d #if str($strand_type.single_type) == "s" @@ -33,9 +31,7 @@ '+-,-+' #end if #end if - @MULTIHITS@ - $onlyexonic --single-read="${singleread}" ]]> @@ -55,14 +51,26 @@ </inputs> <outputs> - <data format="xls" name="outputxls" from_work_dir="output.FPKM.xls"/> + <data format="tabular" name="output" from_work_dir="output.FPKM.xls" label="${tool.name} on ${on_string}: FPKM counts"/> </outputs> <tests> <test> <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/> <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/> - <output name="outputxls" file="output.FPKM.xls"/> + <output name="output" file="output01.tab"/> + </test> + <test> + <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/> + <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/> + <conditional name="multihits_type"> + <param name="multihits_type_selector" value="skip_multihits"/> + <param name="mapq" value="20"/> + </conditional> + <output name="output" file="output02.tab"/> + <assert_command> + <has_text text="--mapq=20" /> + </assert_command> </test> </tests>
--- a/RPKM_saturation.xml Sat Dec 10 11:23:05 2022 +0000 +++ b/RPKM_saturation.xml Wed Feb 22 15:06:01 2023 +0000 @@ -51,8 +51,8 @@ <outputs> <expand macro="pdf_output_data" filename="output.saturation.pdf" /> - <data format="xls" name="outputxls" from_work_dir="output.eRPKM.xls" label="${tool.name} on ${on_string} (RPKM xls)"/> - <data format="xls" name="outputrawxls" from_work_dir="output.rawCount.xls" label="${tool.name} on ${on_string} (Raw Count xls)"/> + <data format="tabular" name="outputxls" from_work_dir="output.eRPKM.xls" label="${tool.name} on ${on_string}: RPKM"/> + <data format="tabular" name="outputrawxls" from_work_dir="output.rawCount.xls" label="${tool.name} on ${on_string}: raw count"/> <expand macro="rscript_output_data" filename="output.saturation.r" /> </outputs>
--- a/clipping_profile.xml Sat Dec 10 11:23:05 2022 +0000 +++ b/clipping_profile.xml Wed Feb 22 15:06:01 2023 +0000 @@ -37,13 +37,13 @@ <test> <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" /> <output name="outputpdf" file="output.clipping_profile.pdf" compare="sim_size" /> - <output name="outputxls" file="output.clipping_profile.xls" /> + <output name="outputxls" file="output.clipping_profile.xls" ftype="tabular"/> </test> <test> <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" /> <param name="rscript_output" value="true" /> <output name="outputpdf" file="output.clipping_profile.pdf" compare="sim_size" /> - <output name="outputxls" file="output.clipping_profile.xls" /> + <output name="outputxls" file="output.clipping_profile.xls" ftype="tabular"/> <output name="outputr" file="output.clipping_profile_r" /> </test> </tests>
--- a/deletion_profile.xml Sat Dec 10 11:23:05 2022 +0000 +++ b/deletion_profile.xml Wed Feb 22 15:06:01 2023 +0000 @@ -40,7 +40,7 @@ <param name="read_align_length" value="101" /> <param name="rscript_output" value="true" /> <output name="outputpdf" file="output.deletion_profile.pdf" compare="sim_size" /> - <output name="outputxls" file="output.deletion_profile.txt" /> + <output name="outputxls" file="output.deletion_profile.txt" ftype="tabular"/> <output name="outputr" file="output.deletion_profile_r" /> </test> </tests>
--- a/insertion_profile.xml Sat Dec 10 11:23:05 2022 +0000 +++ b/insertion_profile.xml Wed Feb 22 15:06:01 2023 +0000 @@ -38,7 +38,7 @@ <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" /> <param name="rscript_output" value="true" /> <output name="outputpdf" file="output.insertion_profile.pdf" compare="sim_size" /> - <output name="outputxls" file="output.insertion_profile.xls" /> + <output name="outputxls" file="output.insertion_profile.xls" ftype="tabular"/> <output name="outputr" file="output.insertion_profile_r" /> </test> </tests>
--- a/junction_annotation.xml Sat Dec 10 11:23:05 2022 +0000 +++ b/junction_annotation.xml Wed Feb 22 15:06:01 2023 +0000 @@ -51,7 +51,7 @@ <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" /> <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/> <param name="rscript_output" value="true" /> - <output name="outputxls" file="output.junction.xls" /> + <output name="outputxls" file="output.junction.xls" ftype="tabular"/> <output name="outputr" file="output.junction_plot_r" /> <output name="outputpdf" file="output.splice_events.pdf" compare="sim_size" /> <output name="outputjpdf" file="output.splice_junction.pdf" compare="sim_size" />
--- a/mismatch_profile.xml Sat Dec 10 11:23:05 2022 +0000 +++ b/mismatch_profile.xml Wed Feb 22 15:06:01 2023 +0000 @@ -39,7 +39,7 @@ <param name="read_align_length" value="101" /> <param name="rscript_output" value="true" /> <output name="outputpdf" file="output.mismatch_profile.pdf" compare="sim_size" /> - <output name="outputxls" file="output.mismatch_profile.xls"/> + <output name="outputxls" file="output.mismatch_profile.xls" ftype="tabular"/> <output name="outputr" file="output.mismatch_profile_r"/> </test> </tests>
--- a/read_GC.xml Sat Dec 10 11:23:05 2022 +0000 +++ b/read_GC.xml Wed Feb 22 15:06:01 2023 +0000 @@ -36,7 +36,7 @@ <test> <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" /> <param name="rscript_output" value="true" /> - <output name="outputxls" file="output.GC.xls" /> + <output name="outputxls" file="output.GC.xls" ftype="tabular"/> <output name="outputr" file="output.GC_plot_r" /> <output name="outputpdf" file="output.GC_plot.pdf" compare="sim_size" /> </test>
--- a/read_NVC.xml Sat Dec 10 11:23:05 2022 +0000 +++ b/read_NVC.xml Wed Feb 22 15:06:01 2023 +0000 @@ -38,7 +38,7 @@ <test> <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" /> <param name="rscript_output" value="true" /> - <output name="outputxls" file="output.NVC.xls" /> + <output name="outputxls" file="output.NVC.xls" ftype="tabular"/> <output name="outputr" file="output.NVC_plot_r" /> <output name="outputpdf" file="output.NVC_plot.pdf" compare="sim_size" /> </test>
--- a/read_duplication.xml Sat Dec 10 11:23:05 2022 +0000 +++ b/read_duplication.xml Wed Feb 22 15:06:01 2023 +0000 @@ -26,8 +26,8 @@ <outputs> <expand macro="pdf_output_data" filename="output.DupRate_plot.pdf" label="${tool.name} on ${on_string}: plot (PDF)"/> - <data format="xls" name="outputxls" from_work_dir="output.pos.DupRate.xls" label="${tool.name} on ${on_string}: positon (XLS)"/> - <data format="xls" name="outputseqxls" from_work_dir="output.seq.DupRate.xls" label="${tool.name} on ${on_string}: sequences (XLS)"/> + <data format="tabular" name="outputxls" from_work_dir="output.pos.DupRate.xls" label="${tool.name} on ${on_string}: positon"/> + <data format="tabular" name="outputseqxls" from_work_dir="output.seq.DupRate.xls" label="${tool.name} on ${on_string}: sequences"/> <expand macro="rscript_output_data" filename="output.DupRate_plot.r" label="${tool.name} on ${on_string}: Rscript"/> </outputs> @@ -35,8 +35,8 @@ <test> <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" /> <param name="rscript_output" value="true" /> - <output name="outputxls" file="output.pos.DupRate.xls" /> - <output name="outputseqxls" file="output.seq.DupRate.xls" /> + <output name="outputxls" file="output.pos.DupRate.xls" ftype="tabular"/> + <output name="outputseqxls" file="output.seq.DupRate.xls" ftype="tabular"/> <output name="outputr" file="output.DupRate_plot_r" /> <output name="outputpdf" file="output.DupRate_plot.pdf" compare="sim_size" /> </test>
--- a/rseqc_macros.xml Sat Dec 10 11:23:05 2022 +0000 +++ b/rseqc_macros.xml Wed Feb 22 15:06:01 2023 +0000 @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">5.0.1</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@VERSION_SUFFIX@">2</token> <token name="@GALAXY_VERSION@">20.01</token> <xml name="requirements"> <requirements> @@ -110,7 +110,7 @@ </xml> <xml name="xls_output_data" token_filename="output.xls" token_label="${tool.name} on ${on_string}: XLS"> - <data format="xls" name="outputxls" from_work_dir="@FILENAME@" label="@LABEL@" /> + <data format="tabular" name="outputxls" from_work_dir="@FILENAME@" label="@LABEL@" /> </xml> <xml name="rscript_output_data" token_filename="output.r" token_label="${tool.name} on ${on_string}: Rscript">
--- a/test-data/output.FPKM.xls Sat Dec 10 11:23:05 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,8 +0,0 @@ -#chrom st end accession mRNA_size gene_strand Frag_count FPM FPKM -chr1 11873 14409 NR_046018 1652.0 + 1.0 50000.0 30266.34382566586 -chr1 14361 29370 NR_024540 1769.0 - 2.0 100000.0 56529.11249293386 -chr1 17368 17436 NR_106918 68.0 - 0.0 0.0 0.0 -chr1 17368 17436 NR_107062 68.0 - 0.0 0.0 0.0 -chr1 34610 36081 NR_026818 1130.0 - 0.0 0.0 0.0 -chr1 34610 36081 NR_026820 1130.0 - 0.0 0.0 0.0 -chr1 69090 70008 NM_001005484 918.0 + 0.0 0.0 0.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output01.tab Wed Feb 22 15:06:01 2023 +0000 @@ -0,0 +1,8 @@ +#chrom st end accession mRNA_size gene_strand Frag_count FPM FPKM +chr1 11873 14409 NR_046018 1652.0 + 1.0 50000.0 30266.34382566586 +chr1 14361 29370 NR_024540 1769.0 - 2.0 100000.0 56529.11249293386 +chr1 17368 17436 NR_106918 68.0 - 0.0 0.0 0.0 +chr1 17368 17436 NR_107062 68.0 - 0.0 0.0 0.0 +chr1 34610 36081 NR_026818 1130.0 - 0.0 0.0 0.0 +chr1 34610 36081 NR_026820 1130.0 - 0.0 0.0 0.0 +chr1 69090 70008 NM_001005484 918.0 + 0.0 0.0 0.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output02.tab Wed Feb 22 15:06:01 2023 +0000 @@ -0,0 +1,8 @@ +#chrom st end accession mRNA_size gene_strand Frag_count FPM FPKM +chr1 11873 14409 NR_046018 1652.0 + 1.0 50000.0 30266.34382566586 +chr1 14361 29370 NR_024540 1769.0 - 2.0 100000.0 56529.11249293386 +chr1 17368 17436 NR_106918 68.0 - 0.0 0.0 0.0 +chr1 17368 17436 NR_107062 68.0 - 0.0 0.0 0.0 +chr1 34610 36081 NR_026818 1130.0 - 0.0 0.0 0.0 +chr1 34610 36081 NR_026820 1130.0 - 0.0 0.0 0.0 +chr1 69090 70008 NM_001005484 918.0 + 0.0 0.0 0.0
--- a/tin.xml Sat Dec 10 11:23:05 2022 +0000 +++ b/tin.xml Wed Feb 22 15:06:01 2023 +0000 @@ -53,7 +53,7 @@ <outputs> <data name="outputsummary" format="tabular" from_work_dir="summary.tab" label="TIN on ${on_string} (summary)" /> - <data name="outputxls" format="xls" from_work_dir="tin.xls" label="TIN on ${on_string} (tin)" /> + <data name="outputxls" format="tabular" from_work_dir="tin.xls" label="TIN on ${on_string} (tin)" /> </outputs> <!-- PDF Files contain R version, must avoid checking for diff --> @@ -62,7 +62,7 @@ <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/> <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/> <output name="outputsummary" file="summary.tin.txt" ftype="tabular"/> - <output name="outputxls" file="output.tin.xls" ftype="xls"/> + <output name="outputxls" file="output.tin.xls" ftype="tabular"/> </test> </tests>