Mercurial > repos > nilesh > rseqc
changeset 63:27e16a30667a draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit d7544582d5599c67a284faf9232cd2ccc4daa1de
author | iuc |
---|---|
date | Tue, 09 Apr 2024 11:24:55 +0000 |
parents | 473382134e56 |
children | |
files | FPKM_count.xml RNA_fragment_size.xml RPKM_saturation.xml bam2wig.xml bam_stat.xml clipping_profile.xml deletion_profile.xml geneBody_coverage.xml infer_experiment.xml inner_distance.xml insertion_profile.xml junction_annotation.xml junction_saturation.xml mismatch_profile.xml read_GC.xml read_NVC.xml read_distribution.xml read_duplication.xml read_hexamer.xml read_quality.xml rseqc_macros.xml tin.xml |
diffstat | 22 files changed, 341 insertions(+), 580 deletions(-) [+] |
line wrap: on
line diff
--- a/FPKM_count.xml Wed Feb 22 15:06:01 2023 +0000 +++ b/FPKM_count.xml Tue Apr 09 11:24:55 2024 +0000 @@ -3,15 +3,10 @@ <macros> <import>rseqc_macros.xml</import> </macros> - <expand macro="bio_tools"/> - - <expand macro="requirements" /> - - <expand macro="stdio" /> - + <expand macro="requirements"/> + <expand macro="stdio"/> <version_command><![CDATA[FPKM_count.py --version]]></version_command> - <command><![CDATA[ @BAM_SAM_INPUTS@ FPKM_count.py -i 'input.${extension}' -o output -r '${refgene}' @@ -36,12 +31,11 @@ --single-read="${singleread}" ]]> </command> - <inputs> - <expand macro="bam_param" /> - <expand macro="refgene_param" /> - <expand macro="strand_type_param" /> - <expand macro="multihits_param" /> + <expand macro="bam_param"/> + <expand macro="refgene_param"/> + <expand macro="strand_type_param"/> + <expand macro="multihits_param"/> <param name="onlyexonic" type="boolean" value="false" truevalue="--only-exonic" falsevalue="" label="Only use exonic (UTR exons and CDS exons) reads, otherwise use all reads" help="(--only-exonic)"/> <param name="singleread" type="select" label="How should read-pairs that only have one end mapped be counted?" help="(--single-read)"> <option value="1" selected="true">Treat it as a whole fragment (1)</option> @@ -49,18 +43,16 @@ <option value="0">Ignore it (0)</option> </param> </inputs> - <outputs> <data format="tabular" name="output" from_work_dir="output.FPKM.xls" label="${tool.name} on ${on_string}: FPKM counts"/> </outputs> - <tests> - <test> + <test expect_num_outputs="1"> <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/> <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/> <output name="output" file="output01.tab"/> </test> - <test> + <test expect_num_outputs="1"> <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/> <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/> <conditional name="multihits_type"> @@ -69,11 +61,10 @@ </conditional> <output name="output" file="output02.tab"/> <assert_command> - <has_text text="--mapq=20" /> + <has_text text="--mapq=20"/> </assert_command> </test> </tests> - <help><![CDATA[ FPKM_count.py +++++++++++++ @@ -134,7 +125,5 @@ ]]> </help> - - <expand macro="citations" /> - + <expand macro="citations"/> </tool>
--- a/RNA_fragment_size.xml Wed Feb 22 15:06:01 2023 +0000 +++ b/RNA_fragment_size.xml Tue Apr 09 11:24:55 2024 +0000 @@ -6,49 +6,41 @@ <import>rseqc_macros.xml</import> </macros> <expand macro="bio_tools"/> - - <expand macro="requirements" /> - - <expand macro="stdio" /> - + <expand macro="requirements"/> + <expand macro="stdio"/> <version_command><![CDATA[RNA_fragment_size.py --version]]></version_command> - <command><![CDATA[ @BAM_SAM_INPUTS@ RNA_fragment_size.py -i 'input.${extension}' --refgene='${refgene}' --mapq=${mapq} --frag-num=${fragnum} > '${output}' ]]> </command> - <inputs> - <expand macro="bam_param" /> - <expand macro="refgene_param" /> - <expand macro="mapq_param" /> - <param name="fragnum" type="integer" value="3" label="Minimum number of fragments (default: 3)" help="(--frag-num)" /> + <expand macro="bam_param"/> + <expand macro="refgene_param"/> + <expand macro="mapq_param"/> + <param name="fragnum" type="integer" value="3" label="Minimum number of fragments (default: 3)" help="(--frag-num)"/> </inputs> - <outputs> - <data format="tabular" name="output" /> + <data format="tabular" name="output"/> </outputs> - <tests> - <test> - <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" /> + <test expect_num_outputs="1"> + <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="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$" /> - <has_line_matching expression="^chr1\t69090\t70008\tNM_001005484\t0\t0\t0\t0$" /> + <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> - <help><![CDATA[ RNA_fragment_size.py ++++++++++++++++++++ @@ -80,7 +72,5 @@ ]]> </help> - - <expand macro="citations" /> - + <expand macro="citations"/> </tool>
--- a/RPKM_saturation.xml Wed Feb 22 15:06:01 2023 +0000 +++ b/RPKM_saturation.xml Tue Apr 09 11:24:55 2024 +0000 @@ -4,13 +4,9 @@ <import>rseqc_macros.xml</import> </macros> <expand macro="bio_tools"/> - - <expand macro="requirements" /> - - <expand macro="stdio" /> - + <expand macro="requirements"/> + <expand macro="stdio"/> <version_command><![CDATA[RPKM_saturation.py --version]]></version_command> - <command><![CDATA[ @BAM_SAM_INPUTS@ RPKM_saturation.py -i 'input.${extension}' -o output -r '${refgene}' @@ -36,53 +32,49 @@ -l ${percentileFloor} -u ${percentileCeiling} -s ${percentileStep} -c ${rpkmCutoff} --mapq $mapq ]]></command> - <inputs> - <expand macro="bam_sam_param" /> - <expand macro="refgene_param" /> - <expand macro="strand_type_param" /> + <expand macro="bam_sam_param"/> + <expand macro="refgene_param"/> + <expand macro="strand_type_param"/> <param name="percentileFloor" type="integer" value="5" label="Begin sampling from this percentile (default=5)" help="(--percentile-floor)"/> - <param name="percentileCeiling" type="integer" value="100" label="End sampling at this percentile (default=100)" help="(--percentile-ceiling)" /> - <param name="percentileStep" type="integer" value="5" label="Sampling step size (default=5)" help="(--percentile-step)" /> - <param name="rpkmCutoff" type="text" value="0.01" label="Ignore transcripts with RPKM smaller than this number (default=0.01)" help="(--rpkm-cutoff)" /> - <expand macro="mapq_param" /> - <expand macro="rscript_output_param" /> + <param name="percentileCeiling" type="integer" value="100" label="End sampling at this percentile (default=100)" help="(--percentile-ceiling)"/> + <param name="percentileStep" type="integer" value="5" label="Sampling step size (default=5)" help="(--percentile-step)"/> + <param name="rpkmCutoff" type="text" value="0.01" label="Ignore transcripts with RPKM smaller than this number (default=0.01)" help="(--rpkm-cutoff)"/> + <expand macro="mapq_param"/> + <expand macro="rscript_output_param"/> </inputs> - <outputs> - <expand macro="pdf_output_data" filename="output.saturation.pdf" /> + <expand macro="pdf_output_data" filename="output.saturation.pdf"/> <data format="tabular" name="outputxls" from_work_dir="output.eRPKM.xls" label="${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" /> + <expand macro="rscript_output_data" filename="output.saturation.r"/> </outputs> - <tests> - <test> + <test expect_num_outputs="4"> <param name="input" value="pairend_strandspecific_51mer_hg19_random.bam"/> <param name="refgene" value="hg19.HouseKeepingGenes_30.bed"/> - <param name="rscript_output" value="true" /> + <param name="rscript_output" value="true"/> <output name="outputxls"> - <assert_contents> - <has_n_columns n="26" /> - <has_line_matching expression="chr1\t16174358\t16266950\tNM_015001.*" /> - </assert_contents> + <assert_contents> + <has_n_columns n="26"/> + <has_line_matching expression="chr1\t16174358\t16266950\tNM_015001.*"/> + </assert_contents> </output> <output name="outputrawxls"> - <assert_contents> - <has_n_columns n="26" /> - <has_line_matching expression="chr1\t16174358\t16266950\tNM_015001.*" /> - </assert_contents> + <assert_contents> + <has_n_columns n="26"/> + <has_line_matching expression="chr1\t16174358\t16266950\tNM_015001.*"/> + </assert_contents> </output> <output name="outputr"> - <assert_contents> - <has_text text="pdf('output.saturation.pdf')" /> - <has_line_matching expression="S5=c\(\d+\.\d+\)" /> - </assert_contents> + <assert_contents> + <has_text text="pdf('output.saturation.pdf')"/> + <has_line_matching expression="S5=c\(\d+\.\d+\)"/> + </assert_contents> </output> - <output name="outputpdf" file="output.saturation.pdf" compare="sim_size" /> + <output name="outputpdf" file="output.saturation.pdf" compare="sim_size"/> </test> </tests> - <help><![CDATA[ RPKM_saturation.py ++++++++++++++++++ @@ -163,7 +155,5 @@ ]]> </help> - - <expand macro="citations" /> - + <expand macro="citations"/> </tool>
--- a/bam2wig.xml Wed Feb 22 15:06:01 2023 +0000 +++ b/bam2wig.xml Tue Apr 09 11:24:55 2024 +0000 @@ -1,19 +1,14 @@ <tool id="rseqc_bam2wig" name="BAM to Wiggle" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@"> <description> - converts all types of RNA-seq data from .bam to .wig + converts all types of RNA-seq data from BAM to Wiggle </description> <macros> <import>rseqc_macros.xml</import> </macros> - <expand macro="bio_tools"/> - - <expand macro="requirements" /> - - <expand macro="stdio" /> - + <expand macro="requirements"/> + <expand macro="stdio"/> <version_command><![CDATA[bam2wig.py --version]]></version_command> - <command><![CDATA[ @BAM_SAM_INPUTS@ bam2wig.py -i 'input.${extension}' -s '${chromsize}' -o outfile @@ -44,9 +39,9 @@ ]]> </command> <inputs> - <expand macro="bam_param" /> + <expand macro="bam_param"/> <param name="chromsize" type="data" label="Chromosome size file (tab or space separated)" format="txt,tabular" help="(--chromSize)"/> - <expand macro="multihits_param" /> + <expand macro="multihits_param"/> <conditional name="wigsum_type"> <param name="wigsum_type_selector" type="select" label="Normalization"> <option value="normalize">Normalize to specified sum</option> @@ -57,9 +52,8 @@ </when> <when value="raw"/> </conditional> - <expand macro="strand_type_param" /> + <expand macro="strand_type_param"/> </inputs> - <outputs> <data format="wig" name="output" from_work_dir="outfile.wig"> <filter>strand_type['strand_specific'] == 'none'</filter> @@ -71,21 +65,20 @@ <filter>strand_type['strand_specific'] != 'none'</filter> </data> </outputs> - <tests> - <test> + <test expect_num_outputs="1"> <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/> <param name="chromsize" value="hg19.chrom.sizes"/> <output name="output" file="testwig.wig"/> </test> - <test> + <test expect_num_outputs="1"> <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/> <param name="chromsize" value="hg19.chrom.sizes"/> <param name="multihits_type_selector" value="skip_multihits"/> <param name="mapq" value="20"/> <output name="output" file="testwig.wig"/> </test> - <test> + <test expect_num_outputs="2"> <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/> <param name="chromsize" value="hg19.chrom.sizes"/> <param name="strand_specific" value="pair"/> @@ -93,7 +86,7 @@ <output name="outputfwd" file="testwig.Forward.wig"/> <output name="outputrv" file="testwig.Reverse.wig"/> </test> - <test> + <test expect_num_outputs="1"> <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/> <param name="chromsize" value="hg19.chrom.sizes"/> <param name="wigsum_type_selector" value="normalize"/> @@ -101,7 +94,6 @@ <output name="output" file="testwig_wigsum100.wig"/> </test> </tests> - <help><![CDATA[ bam2wig.py ++++++++++ @@ -149,7 +141,5 @@ .. _bigwig: http://genome.ucsc.edu/FAQ/FAQformat.html#format6.1 ]]> </help> - - <expand macro="citations" /> - + <expand macro="citations"/> </tool>
--- a/bam_stat.xml Wed Feb 22 15:06:01 2023 +0000 +++ b/bam_stat.xml Tue Apr 09 11:24:55 2024 +0000 @@ -5,37 +5,28 @@ <macros> <import>rseqc_macros.xml</import> </macros> - <expand macro="bio_tools"/> - - <expand macro="requirements" /> - - <expand macro="stdio" /> - + <expand macro="requirements"/> + <expand macro="stdio"/> <version_command><![CDATA[bam_stat.py --version]]></version_command> - <command><![CDATA[ @BAM_SAM_INPUTS@ bam_stat.py -i 'input.${extension}' -q ${mapq} > '${output}' ]]> </command> - <inputs> - <expand macro="bam_sam_param" /> - <expand macro="mapq_param" /> + <expand macro="bam_sam_param"/> + <expand macro="mapq_param"/> </inputs> - <outputs> <data format="txt" name="output" label="${tool.name} on ${on_string}: stats"/> </outputs> - <tests> <test> - <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" /> - <output name="output" file="output.bamstats.txt" /> + <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/> + <output name="output" file="output.bamstats.txt"/> </test> </tests> - <help><![CDATA[ bam_stat.py +++++++++++ @@ -68,6 +59,5 @@ ]]> </help> - - <expand macro="citations" /> + <expand macro="citations"/> </tool>
--- a/clipping_profile.xml Wed Feb 22 15:06:01 2023 +0000 +++ b/clipping_profile.xml Tue Apr 09 11:24:55 2024 +0000 @@ -5,49 +5,40 @@ <macros> <import>rseqc_macros.xml</import> </macros> - <expand macro="bio_tools"/> - - <expand macro="requirements" /> - - <expand macro="stdio" /> - + <expand macro="requirements"/> + <expand macro="stdio"/> <version_command><![CDATA[clipping_profile.py --version]]></version_command> - <command><![CDATA[ @BAM_SAM_INPUTS@ clipping_profile.py -i 'input.${extension}' -o output -q ${mapq} -s "${layout}" ]]> </command> - <inputs> - <expand macro="bam_param" /> - <expand macro="mapq_param" /> - <expand macro="layout_param" /> - <expand macro="rscript_output_param" /> + <expand macro="bam_param"/> + <expand macro="mapq_param"/> + <expand macro="layout_param"/> + <expand macro="rscript_output_param"/> </inputs> - <outputs> <expand macro="pdf_output_data" filename="output.clipping_profile.pdf" label="${tool.name} on ${on_string}: PDF"/> <expand macro="xls_output_data" filename="output.clipping_profile.xls" label="${tool.name} on ${on_string}: XML"/> <expand macro="rscript_output_data" filename="output.clipping_profile.r" label="${tool.name} on ${on_string}: Rscript"/> </outputs> - <tests> - <test> - <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" /> - <output name="outputpdf" file="output.clipping_profile.pdf" compare="sim_size" /> + <test expect_num_outputs="2"> + <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/> + <output name="outputpdf" file="output.clipping_profile.pdf" compare="sim_size"/> <output name="outputxls" file="output.clipping_profile.xls" ftype="tabular"/> </test> - <test> - <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" /> - <param name="rscript_output" value="true" /> - <output name="outputpdf" file="output.clipping_profile.pdf" compare="sim_size" /> + <test expect_num_outputs="3"> + <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/> + <param name="rscript_output" value="true"/> + <output name="outputpdf" file="output.clipping_profile.pdf" compare="sim_size"/> <output name="outputxls" file="output.clipping_profile.xls" ftype="tabular"/> - <output name="outputr" file="output.clipping_profile_r" /> + <output name="outputr" file="output.clipping_profile_r"/> </test> </tests> - <help><![CDATA[ clipping_profile.py +++++++++++++++++++ @@ -81,7 +72,5 @@ ]]> </help> - - <expand macro="citations" /> - + <expand macro="citations"/> </tool>
--- a/deletion_profile.xml Wed Feb 22 15:06:01 2023 +0000 +++ b/deletion_profile.xml Tue Apr 09 11:24:55 2024 +0000 @@ -5,46 +5,37 @@ <macros> <import>rseqc_macros.xml</import> </macros> - <expand macro="bio_tools"/> - - <expand macro="requirements" /> - - <expand macro="stdio" /> - + <expand macro="requirements"/> + <expand macro="stdio"/> <version_command><![CDATA[deletion_profile.py --version]]></version_command> - <command><![CDATA[ @BAM_SAM_INPUTS@ deletion_profile.py -i 'input.${extension}' -o output -l ${read_align_length} -n ${read_num} -q ${mapq} ]]> </command> - <inputs> - <expand macro="bam_param" /> - <expand macro="readlength_param" /> - <expand macro="readnum_param" /> - <expand macro="mapq_param" /> - <expand macro="rscript_output_param" /> + <expand macro="bam_param"/> + <expand macro="readlength_param"/> + <expand macro="readnum_param"/> + <expand macro="mapq_param"/> + <expand macro="rscript_output_param"/> </inputs> - <outputs> - <expand macro="pdf_output_data" filename="output.deletion_profile.pdf" /> - <expand macro="xls_output_data" filename="output.deletion_profile.txt" /> - <expand macro="rscript_output_data" filename="output.deletion_profile.r" /> + <expand macro="pdf_output_data" filename="output.deletion_profile.pdf"/> + <expand macro="xls_output_data" filename="output.deletion_profile.txt"/> + <expand macro="rscript_output_data" filename="output.deletion_profile.r"/> </outputs> - <tests> - <test> - <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" /> - <param name="read_align_length" value="101" /> - <param name="rscript_output" value="true" /> - <output name="outputpdf" file="output.deletion_profile.pdf" compare="sim_size" /> + <test expect_num_outputs="3"> + <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/> + <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" ftype="tabular"/> - <output name="outputr" file="output.deletion_profile_r" /> + <output name="outputr" file="output.deletion_profile_r"/> </test> </tests> - <help><![CDATA[ deletion_profile.py +++++++++++++++++++ @@ -83,7 +74,5 @@ ]]> </help> - - <expand macro="citations" /> - + <expand macro="citations"/> </tool>
--- a/geneBody_coverage.xml Wed Feb 22 15:06:01 2023 +0000 +++ b/geneBody_coverage.xml Tue Apr 09 11:24:55 2024 +0000 @@ -4,8 +4,8 @@ <import>rseqc_macros.xml</import> </macros> <expand macro="bio_tools"/> - <expand macro="requirements" /> - <expand macro="stdio" /> + <expand macro="requirements"/> + <expand macro="stdio"/> <version_command><![CDATA[geneBody_coverage.py --version]]></version_command> <command><![CDATA[ #if str($batch_mode.batch_mode_selector) == "merge": @@ -30,63 +30,58 @@ #end if ]]> </command> - - <inputs> - <conditional name="batch_mode"> - <param name="batch_mode_selector" type="select" label="Run each sample separately, or combine mutiple samples into one plot"> - <option value="batch" selected="true">Run each sample separately</option> - <option value="merge">Combine multiple samples into a single plot</option> - </param> - <when value="batch"> - <param name="input" type="data" label="Input .bam file" format="bam" help="(--input-file)"/> - </when> - <when value="merge"> - <param name="inputs" type="data" label="Input .bam file(s)" format="bam" help="(--input-file)" multiple="true"/> - </when> - </conditional> - <expand macro="refgene_param" /> - <param name="minimum_length" type="integer" value="100" label="Minimum mRNA length (default: 100)" help="Minimum mRNA length in bp, mRNA that are shorter than this value will be skipped (--minimum_length)." /> - <expand macro="rscript_output_param" /> - </inputs> - - <outputs> - <data name="outputcurvespdf" format="pdf" from_work_dir="output.geneBodyCoverage.curves.pdf" label="${tool.name} on ${on_string}: curves (PDF)" /> - <data name="outputheatmappdf" format="pdf" from_work_dir="output.geneBodyCoverage.heatMap.pdf" label="${tool.name} on ${on_string}: heatmap (PDF)"> - <filter>batch_mode['batch_mode_selector'] == 'merge' and len(inputs) >= 3</filter> - </data> - <expand macro="rscript_output_data" filename="output.geneBodyCoverage.r" label="${tool.name} on ${on_string}: Rscript"/> - <data name="outputtxt" format="txt" from_work_dir="output.geneBodyCoverage.txt" label="${tool.name} on ${on_string}: stats (TXT)" /> - </outputs> - - <!-- PDF Files contain R version, must avoid checking for diff --> - <tests> - <test> - <conditional name="batch_mode"> - <param name="batch_mode_selector" value="batch" /> - <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" /> - </conditional> - <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" /> - <param name="rscript_output" value="true" /> - <output name="outputcurvespdf" file="output.geneBodyCoverage.curves.pdf" compare="sim_size" /> - <output name="outputr" file="output.geneBodyCoverage_r" /> - <output name="outputtxt" file="output.geneBodyCoverage.txt" /> - </test> - <test> - <conditional name="batch_mode"> - <param name="batch_mode_selector" value="merge" /> - <param name="inputs" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam,pairend_strandspecific_51mer_hg19_chr1_1-100000.bam,pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" /> - </conditional> - <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/> - <param name="rscript_output" value="true" /> - <output name="outputcurvespdf" file="output2.geneBodyCoverage.curves.pdf" compare="sim_size" /> - <output name="outputheatmappdf" file="output2.geneBodyCoverage.heatMap.pdf" compare="sim_size" /> - <output name="outputr" file="output2.geneBodyCoverage_r" /> - <output name="outputtxt" file="output2.geneBodyCoverage.txt" /> - </test> - - </tests> - - <help><![CDATA[ + <inputs> + <conditional name="batch_mode"> + <param name="batch_mode_selector" type="select" label="Run each sample separately, or combine mutiple samples into one plot"> + <option value="batch" selected="true">Run each sample separately</option> + <option value="merge">Combine multiple samples into a single plot</option> + </param> + <when value="batch"> + <param name="input" type="data" label="Input .bam file" format="bam" help="(--input-file)"/> + </when> + <when value="merge"> + <param name="inputs" type="data" label="Input .bam file(s)" format="bam" help="(--input-file)" multiple="true"/> + </when> + </conditional> + <expand macro="refgene_param"/> + <param name="minimum_length" type="integer" value="100" label="Minimum mRNA length (default: 100)" help="Minimum mRNA length in bp, mRNA that are shorter than this value will be skipped (--minimum_length)."/> + <expand macro="rscript_output_param"/> + </inputs> + <outputs> + <data name="outputcurvespdf" format="pdf" from_work_dir="output.geneBodyCoverage.curves.pdf" label="${tool.name} on ${on_string}: curves (PDF)"/> + <data name="outputheatmappdf" format="pdf" from_work_dir="output.geneBodyCoverage.heatMap.pdf" label="${tool.name} on ${on_string}: heatmap (PDF)"> + <filter>batch_mode['batch_mode_selector'] == 'merge' and len(inputs) >= 3</filter> + </data> + <expand macro="rscript_output_data" filename="output.geneBodyCoverage.r" label="${tool.name} on ${on_string}: Rscript"/> + <data name="outputtxt" format="txt" from_work_dir="output.geneBodyCoverage.txt" label="${tool.name} on ${on_string}: stats (TXT)"/> + </outputs> + <!-- PDF Files contain R version, must avoid checking for diff --> + <tests> + <test expect_num_outputs="3"> + <conditional name="batch_mode"> + <param name="batch_mode_selector" value="batch"/> + <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/> + </conditional> + <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed"/> + <param name="rscript_output" value="true"/> + <output name="outputcurvespdf" file="output.geneBodyCoverage.curves.pdf" compare="sim_size"/> + <output name="outputr" file="output.geneBodyCoverage_r"/> + <output name="outputtxt" file="output.geneBodyCoverage.txt"/> + </test> + <test expect_num_outputs="4"> + <conditional name="batch_mode"> + <param name="batch_mode_selector" value="merge"/> + <param name="inputs" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam,pairend_strandspecific_51mer_hg19_chr1_1-100000.bam,pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/> + </conditional> + <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/> + <param name="rscript_output" value="true"/> + <output name="outputcurvespdf" file="output2.geneBodyCoverage.curves.pdf" compare="sim_size"/> + <output name="outputheatmappdf" file="output2.geneBodyCoverage.heatMap.pdf" compare="sim_size"/> + <output name="outputr" file="output2.geneBodyCoverage_r"/> + <output name="outputtxt" file="output2.geneBodyCoverage.txt"/> + </test> + </tests> + <help><![CDATA[ ## geneBody_coverage.py Read coverage over gene body. This module is used to check if read coverage is uniform and if there is any 5\'/3\' bias. This module scales all transcripts to 100 nt and calculates the number of reads covering each nucleotide position. Finally, it generates plots illustrating the coverage profile along the gene body. @@ -138,7 +133,5 @@ ]]> </help> - - <expand macro="citations" /> - + <expand macro="citations"/> </tool>
--- a/infer_experiment.xml Wed Feb 22 15:06:01 2023 +0000 +++ b/infer_experiment.xml Tue Apr 09 11:24:55 2024 +0000 @@ -3,15 +3,10 @@ <macros> <import>rseqc_macros.xml</import> </macros> - <expand macro="bio_tools"/> - - <expand macro="requirements" /> - - <expand macro="stdio" /> - + <expand macro="requirements"/> + <expand macro="stdio"/> <version_command><![CDATA[infer_experiment.py --version]]></version_command> - <command><![CDATA[ @BAM_SAM_INPUTS@ infer_experiment.py -i 'input.${extension}' -r '${refgene}' @@ -20,26 +15,22 @@ > '${output}' ]]> </command> - <inputs> - <expand macro="bam_param" /> - <expand macro="refgene_param" /> - <expand macro="sample_size_param" /> - <expand macro="mapq_param" /> + <expand macro="bam_param"/> + <expand macro="refgene_param"/> + <expand macro="sample_size_param"/> + <expand macro="mapq_param"/> </inputs> - <outputs> - <data format="txt" name="output" label="${tool.name} on ${on_string}: RNA-seq experiment configuration" /> + <data format="txt" name="output" label="${tool.name} on ${on_string}: RNA-seq experiment configuration"/> </outputs> - <tests> - <test> + <test expect_num_outputs="1"> <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/> <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/> <output name="output" file="output.infer_experiment.txt"/> </test> </tests> - <help><![CDATA[ infer_experiment.py +++++++++++++++++++ @@ -137,7 +128,5 @@ ]]> </help> - - <expand macro="citations" /> - + <expand macro="citations"/> </tool>
--- a/inner_distance.xml Wed Feb 22 15:06:01 2023 +0000 +++ b/inner_distance.xml Tue Apr 09 11:24:55 2024 +0000 @@ -3,15 +3,10 @@ <macros> <import>rseqc_macros.xml</import> </macros> - <expand macro="bio_tools"/> - - <expand macro="requirements" /> - - <expand macro="stdio" /> - + <expand macro="requirements"/> + <expand macro="stdio"/> <version_command><![CDATA[inner_distance.py --version]]></version_command> - <command><![CDATA[ @BAM_SAM_INPUTS@ inner_distance.py -i 'input.${extension}' -o output -r '${refgene}' @@ -22,37 +17,33 @@ --mapq ${mapq} ]]> </command> - <inputs> - <expand macro="bam_sam_param" /> - <expand macro="refgene_param" /> - <expand macro="sample_size_param" /> + <expand macro="bam_sam_param"/> + <expand macro="refgene_param"/> + <expand macro="sample_size_param"/> <param name="lowerBound" type="integer" value="-250" label="Lower bound (bp, default=-250)" help="Used for plotting histogram (--lower-bound)"/> <param name="upperBound" type="integer" value="250" label="Upper bound (bp, default=250)" help="Used for plotting histogram (--upper-bound)"/> <param name="step" type="integer" value="5" label="Step size of histogram (bp, default=5)" help="(--step)"/> - <expand macro="mapq_param" /> - <expand macro="rscript_output_param" /> + <expand macro="mapq_param"/> + <expand macro="rscript_output_param"/> </inputs> - <outputs> <expand macro="pdf_output_data" filename="output.inner_distance_plot.pdf" label="${tool.name} on ${on_string}: plot (PDF)"/> <data format="txt" name="outputtxt" from_work_dir="output.inner_distance.txt" label="${tool.name} on ${on_string}: TXT"/> - <data format="txt" name="outputfreqtxt" from_work_dir="output.inner_distance_freq.txt" label="${tool.name} on ${on_string}: frequency (TXT)" /> - <expand macro="rscript_output_data" filename="output.inner_distance_plot.r" label="${tool.name} on ${on_string}: Rscript"/> + <data format="txt" name="outputfreqtxt" from_work_dir="output.inner_distance_freq.txt" label="${tool.name} on ${on_string}: frequency (TXT)"/> + <expand macro="rscript_output_data" filename="output.inner_distance_plot.r" label="${tool.name} on ${on_string}: Rscript"/> </outputs> - <tests> - <test> + <test expect_num_outputs="4"> <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/> <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/> - <param name="rscript_output" value="true" /> - <output name="outputtxt" file="output.inner_distance.txt" /> - <output name="outputfreqtxt" file="output.inner_distance_freq.txt" /> + <param name="rscript_output" value="true"/> + <output name="outputtxt" file="output.inner_distance.txt"/> + <output name="outputfreqtxt" file="output.inner_distance_freq.txt"/> <output name="outputpdf" file="output.inner_distance_plot.pdf" compare="sim_size"/> - <output name="outputr" file="output.inner_distance_plot_r" /> + <output name="outputr" file="output.inner_distance_plot_r"/> </test> </tests> - <help><![CDATA[ inner_distance.py +++++++++++++++++ @@ -109,7 +100,5 @@ ]]> </help> - - <expand macro="citations" /> - + <expand macro="citations"/> </tool>
--- a/insertion_profile.xml Wed Feb 22 15:06:01 2023 +0000 +++ b/insertion_profile.xml Tue Apr 09 11:24:55 2024 +0000 @@ -5,44 +5,35 @@ <macros> <import>rseqc_macros.xml</import> </macros> - <expand macro="bio_tools"/> - - <expand macro="requirements" /> - - <expand macro="stdio" /> - + <expand macro="requirements"/> + <expand macro="stdio"/> <version_command><![CDATA[insertion_profile.py --version]]></version_command> - <command><![CDATA[ @BAM_SAM_INPUTS@ insertion_profile.py -i 'input.${extension}' -o output -q ${mapq} -s "${layout}" ]]> </command> - <inputs> - <expand macro="bam_sam_param" /> - <expand macro="mapq_param" /> - <expand macro="layout_param" /> - <expand macro="rscript_output_param" /> + <expand macro="bam_sam_param"/> + <expand macro="mapq_param"/> + <expand macro="layout_param"/> + <expand macro="rscript_output_param"/> </inputs> - <outputs> - <expand macro="pdf_output_data" filename="output.insertion_profile.pdf" /> - <expand macro="xls_output_data" filename="output.insertion_profile.xls" /> - <expand macro="rscript_output_data" filename="output.insertion_profile.r" /> + <expand macro="pdf_output_data" filename="output.insertion_profile.pdf"/> + <expand macro="xls_output_data" filename="output.insertion_profile.xls"/> + <expand macro="rscript_output_data" filename="output.insertion_profile.r"/> </outputs> - <tests> - <test> - <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" /> + <test expect_num_outputs="3"> + <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" ftype="tabular"/> - <output name="outputr" file="output.insertion_profile_r" /> + <output name="outputr" file="output.insertion_profile_r"/> </test> </tests> - <help><![CDATA[ insertion_profile.py ++++++++++++++++++++ @@ -84,7 +75,5 @@ ]]> </help> - - <expand macro="citations" /> - + <expand macro="citations"/> </tool>
--- a/junction_annotation.xml Wed Feb 22 15:06:01 2023 +0000 +++ b/junction_annotation.xml Tue Apr 09 11:24:55 2024 +0000 @@ -3,9 +3,7 @@ <macros> <import>rseqc_macros.xml</import> </macros> - <expand macro="bio_tools"/> - <expand macro="requirements"> <!-- Required due to conda solver bug: https://github.com/conda/conda/issues/6269 @@ -13,11 +11,8 @@ --> <requirement type="package" version="4.2.2">r-base</requirement> </expand> - - <expand macro="stdio" /> - + <expand macro="stdio"/> <version_command><![CDATA[junction_annotation.py --version]]></version_command> - <command><![CDATA[ @BAM_SAM_INPUTS@ junction_annotation.py @@ -29,36 +24,32 @@ 2> >(tee -a stats.txt >&2) ]]> </command> - <inputs> - <expand macro="bam_sam_param" /> - <expand macro="refgene_param" /> - <expand macro="min_intron_param" /> - <expand macro="mapq_param" /> - <expand macro="rscript_output_param" /> + <expand macro="bam_sam_param"/> + <expand macro="refgene_param"/> + <expand macro="min_intron_param"/> + <expand macro="mapq_param"/> + <expand macro="rscript_output_param"/> </inputs> - <outputs> <data format="pdf" name="outputpdf" from_work_dir="output.splice_events.pdf" label="${tool.name} on ${on_string}: splice events (PDF)"/> - <data format="pdf" name="outputjpdf" from_work_dir="output.splice_junction.pdf" label="${tool.name} on ${on_string}: splice junction (PDF)" /> - <expand macro="xls_output_data" filename="output.junction.xls" label="${tool.name} on ${on_string}: splice junction (XLS)" /> + <data format="pdf" name="outputjpdf" from_work_dir="output.splice_junction.pdf" label="${tool.name} on ${on_string}: splice junction (PDF)"/> + <expand macro="xls_output_data" filename="output.junction.xls" label="${tool.name} on ${on_string}: splice junction (XLS)"/> <expand macro="rscript_output_data" filename="output.junction_plot.r" label="${tool.name} on ${on_string}: Rscript"/> - <data format="txt" name="stats" from_work_dir="stats.txt" label="${tool.name} on ${on_string}: stats" /> + <data format="txt" name="stats" from_work_dir="stats.txt" label="${tool.name} on ${on_string}: stats"/> </outputs> - <tests> - <test> - <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" /> + <test expect_num_outputs="5"> + <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" /> + <param name="rscript_output" value="true"/> <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" /> - <output name="stats" file="output.splice_junction.txt" ftype="txt" lines_diff="2" /> + <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"/> + <output name="stats" file="output.splice_junction.txt" ftype="txt" lines_diff="2"/> </test> </tests> - <help><![CDATA[ junction_annotation.py ++++++++++++++++++++++ @@ -112,7 +103,5 @@ ]]> </help> - - <expand macro="citations" /> - + <expand macro="citations"/> </tool>
--- a/junction_saturation.xml Wed Feb 22 15:06:01 2023 +0000 +++ b/junction_saturation.xml Tue Apr 09 11:24:55 2024 +0000 @@ -4,8 +4,8 @@ <import>rseqc_macros.xml</import> </macros> <expand macro="bio_tools"/> - <expand macro="requirements" /> - <expand macro="stdio" /> + <expand macro="requirements"/> + <expand macro="stdio"/> <version_command><![CDATA[junction_saturation.py --version]]></version_command> <command><![CDATA[ @BAM_SAM_INPUTS@ @@ -23,13 +23,12 @@ #end if ]]> </command> - <inputs> - <expand macro="bam_sam_param" /> - <expand macro="refgene_param" /> - <expand macro="min_intron_param" /> - <param name="min_coverage" type="integer" label="Minimum number of supporting reads to call a junction (default=1)" value="1" help="(--min-coverage)" /> - <expand macro="mapq_param" /> + <expand macro="bam_sam_param"/> + <expand macro="refgene_param"/> + <expand macro="min_intron_param"/> + <param name="min_coverage" type="integer" label="Minimum number of supporting reads to call a junction (default=1)" value="1" help="(--min-coverage)"/> + <expand macro="mapq_param"/> <conditional name="percentiles_type"> <param name="percentiles_type_selector" type="select" label="Sampling bounds and frequency"> <option value="default" selected="true">Default sampling bounds and frequency</option> @@ -37,40 +36,37 @@ </param> <when value="specify"> <param name="lowBound" type="integer" value="5" label="Lower Bound Sampling Frequency (bp, default=5)" help="(--percentile-floor)"> - <validator type="in_range" min="0" max="100" /> + <validator type="in_range" min="0" max="100"/> </param> <param name="upBound" type="integer" value="100" label="Upper Bound Sampling Frequency (bp, default=100)" help="(--percentile-ceiling)"> - <validator type="in_range" min="0" max="100" /> + <validator type="in_range" min="0" max="100"/> </param> <param name="percentileStep" type="integer" value="5" label="Sampling increment (default=5)" help="(--percentile-step)"> - <validator type="in_range" min="0" max="100" /> + <validator type="in_range" min="0" max="100"/> </param> </when> <when value="default"/> </conditional> - <expand macro="rscript_output_param" /> + <expand macro="rscript_output_param"/> </inputs> - <outputs> <expand macro="pdf_output_data" filename="output.junctionSaturation_plot.pdf" label="${tool.name} on ${on_string}: junction saturation (PDF)"/> <expand macro="rscript_output_data" filename="output.junctionSaturation_plot.r" label="${tool.name} on ${on_string}: junction saturation (Rscript)"/> </outputs> - <tests> - <test> - <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" /> + <test expect_num_outputs="2"> + <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/> <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/> - <param name="rscript_output" value="true" /> + <param name="rscript_output" value="true"/> <output name="outputr" file="output.junctionSaturation_plot_r" compare="sim_size"> <assert_contents> - <has_line line="pdf('output.junctionSaturation_plot.pdf')" /> - <has_line line="x=c(5,10,15,20,25,30,35,40,45,50,55,60,65,70,75,80,85,90,95,100)" /> + <has_line line="pdf('output.junctionSaturation_plot.pdf')"/> + <has_line line="x=c(5,10,15,20,25,30,35,40,45,50,55,60,65,70,75,80,85,90,95,100)"/> </assert_contents> </output> - <output name="outputpdf" file="output.junctionSaturation_plot.pdf" compare="sim_size" /> + <output name="outputpdf" file="output.junctionSaturation_plot.pdf" compare="sim_size"/> </test> </tests> - <help><![CDATA[ junction_saturation.py ++++++++++++++++++++++ @@ -120,7 +116,5 @@ ]]> </help> - - <expand macro="citations" /> - + <expand macro="citations"/> </tool>
--- a/mismatch_profile.xml Wed Feb 22 15:06:01 2023 +0000 +++ b/mismatch_profile.xml Tue Apr 09 11:24:55 2024 +0000 @@ -6,44 +6,36 @@ <import>rseqc_macros.xml</import> </macros> <expand macro="bio_tools"/> - - <expand macro="requirements" /> - - <expand macro="stdio" /> - + <expand macro="requirements"/> + <expand macro="stdio"/> <version_command><![CDATA[mismatch_profile.py --version]]></version_command> - <command><![CDATA[ @BAM_SAM_INPUTS@ mismatch_profile.py -i 'input.${extension}' -o output -l ${read_align_length} -n ${read_num} -q ${mapq} ]]> </command> - <inputs> - <expand macro="bam_param" /> - <expand macro="readlength_param" /> - <expand macro="readnum_param" /> - <expand macro="mapq_param" /> - <expand macro="rscript_output_param" /> + <expand macro="bam_param"/> + <expand macro="readlength_param"/> + <expand macro="readnum_param"/> + <expand macro="mapq_param"/> + <expand macro="rscript_output_param"/> </inputs> - <outputs> - <expand macro="pdf_output_data" filename="output.mismatch_profile.pdf" /> - <expand macro="xls_output_data" filename="output.mismatch_profile.xls" /> - <expand macro="rscript_output_data" filename="output.mismatch_profile.r" /> + <expand macro="pdf_output_data" filename="output.mismatch_profile.pdf"/> + <expand macro="xls_output_data" filename="output.mismatch_profile.xls"/> + <expand macro="rscript_output_data" filename="output.mismatch_profile.r"/> </outputs> - <tests> - <test> + <test expect_num_outputs="3"> <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/> - <param name="read_align_length" value="101" /> - <param name="rscript_output" value="true" /> - <output name="outputpdf" file="output.mismatch_profile.pdf" compare="sim_size" /> + <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" ftype="tabular"/> <output name="outputr" file="output.mismatch_profile_r"/> </test> </tests> - <help><![CDATA[ mismatch_profile.py +++++++++++++++++++ @@ -84,7 +76,5 @@ ]]> </help> - - <expand macro="citations" /> - + <expand macro="citations"/> </tool>
--- a/read_GC.xml Wed Feb 22 15:06:01 2023 +0000 +++ b/read_GC.xml Tue Apr 09 11:24:55 2024 +0000 @@ -4,13 +4,9 @@ <import>rseqc_macros.xml</import> </macros> <expand macro="bio_tools"/> - - <expand macro="requirements" /> - - <expand macro="stdio" /> - + <expand macro="requirements"/> + <expand macro="stdio"/> <version_command><![CDATA[read_GC.py --version]]></version_command> - <command><![CDATA[ @BAM_SAM_INPUTS@ read_GC.py @@ -19,29 +15,25 @@ --mapq ${mapq} ]]> </command> - <inputs> - <expand macro="bam_sam_param" /> - <expand macro="mapq_param" /> - <expand macro="rscript_output_param" /> + <expand macro="bam_sam_param"/> + <expand macro="mapq_param"/> + <expand macro="rscript_output_param"/> </inputs> - <outputs> <expand macro="pdf_output_data" filename="output.GC_plot.pdf" label="${tool.name} on ${on_string}: plot (PDF)"/> <expand macro="xls_output_data" filename="output.GC.xls" label="${tool.name} on ${on_string}: XLS"/> <expand macro="rscript_output_data" filename="output.GC_plot.r" label="${tool.name} on ${on_string}: Rscript"/> </outputs> - <tests> - <test> - <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" /> - <param name="rscript_output" value="true" /> + <test expect_num_outputs="3"> + <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" ftype="tabular"/> - <output name="outputr" file="output.GC_plot_r" /> - <output name="outputpdf" file="output.GC_plot.pdf" compare="sim_size" /> + <output name="outputr" file="output.GC_plot_r"/> + <output name="outputpdf" file="output.GC_plot.pdf" compare="sim_size"/> </test> </tests> - <help><![CDATA[ read_GC.py ++++++++++ @@ -69,7 +61,5 @@ ]]> </help> - - <expand macro="citations" /> - + <expand macro="citations"/> </tool>
--- a/read_NVC.xml Wed Feb 22 15:06:01 2023 +0000 +++ b/read_NVC.xml Tue Apr 09 11:24:55 2024 +0000 @@ -4,13 +4,9 @@ <import>rseqc_macros.xml</import> </macros> <expand macro="bio_tools"/> - - <expand macro="requirements" /> - - <expand macro="stdio" /> - + <expand macro="requirements"/> + <expand macro="stdio"/> <version_command><![CDATA[read_NVC.py --version]]></version_command> - <command><![CDATA[ @BAM_SAM_INPUTS@ read_NVC.py @@ -20,30 +16,26 @@ --mapq ${mapq} ]]> </command> - <inputs> - <expand macro="bam_sam_param" /> + <expand macro="bam_sam_param"/> <param name="nx" type="boolean" value="false" truevalue="--nx" falsevalue="" label="Include N,X in NVC plot" help="(--nx)"/> - <expand macro="mapq_param" /> - <expand macro="rscript_output_param" /> + <expand macro="mapq_param"/> + <expand macro="rscript_output_param"/> </inputs> - <outputs> - <expand macro="pdf_output_data" filename="output.NVC_plot.pdf" /> - <expand macro="xls_output_data" filename="output.NVC.xls" /> - <expand macro="rscript_output_data" filename="output.NVC_plot.r" /> + <expand macro="pdf_output_data" filename="output.NVC_plot.pdf"/> + <expand macro="xls_output_data" filename="output.NVC.xls"/> + <expand macro="rscript_output_data" filename="output.NVC_plot.r"/> </outputs> - <tests> - <test> - <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" /> - <param name="rscript_output" value="true" /> + <test expect_num_outputs="3"> + <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" ftype="tabular"/> - <output name="outputr" file="output.NVC_plot_r" /> - <output name="outputpdf" file="output.NVC_plot.pdf" compare="sim_size" /> + <output name="outputr" file="output.NVC_plot_r"/> + <output name="outputpdf" file="output.NVC_plot.pdf" compare="sim_size"/> </test> </tests> - <help><![CDATA[ read_NVC.py +++++++++++ @@ -86,7 +78,5 @@ ]]> </help> - - <expand macro="citations" /> - + <expand macro="citations"/> </tool>
--- a/read_distribution.xml Wed Feb 22 15:06:01 2023 +0000 +++ b/read_distribution.xml Tue Apr 09 11:24:55 2024 +0000 @@ -4,36 +4,28 @@ <import>rseqc_macros.xml</import> </macros> <expand macro="bio_tools"/> - - <expand macro="requirements" /> - - <expand macro="stdio" /> - + <expand macro="requirements"/> + <expand macro="stdio"/> <version_command><![CDATA[read_distribution.py --version]]></version_command> - <command><![CDATA[ @BAM_SAM_INPUTS@ read_distribution.py -i 'input.${extension}' -r '${refgene}' > '${output}' ]]> </command> - <inputs> - <expand macro="bam_sam_param" /> - <expand macro="refgene_param" /> + <expand macro="bam_sam_param"/> + <expand macro="refgene_param"/> </inputs> - <outputs> - <data format="txt" name="output" label="${tool.name} on ${on_string}: stats (TXT)"/> + <data format="txt" name="output" label="${tool.name} on ${on_string}: stats (TXT)"/> </outputs> - <tests> - <test> + <test expect_num_outputs="1"> <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/> <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/> <output name="output" file="output.read_distribution.txt"/> </test> </tests> - <help><![CDATA[ read_distribution.py ++++++++++++++++++++ @@ -91,7 +83,5 @@ ]]> </help> - - <expand macro="citations" /> - + <expand macro="citations"/> </tool>
--- a/read_duplication.xml Wed Feb 22 15:06:01 2023 +0000 +++ b/read_duplication.xml Tue Apr 09 11:24:55 2024 +0000 @@ -4,35 +4,28 @@ <import>rseqc_macros.xml</import> </macros> <expand macro="bio_tools"/> - <expand macro="requirements" /> - <expand macro="stdio" /> - <version_command><![CDATA[read_duplication.py --version]]></version_command> - <command><![CDATA[ @BAM_SAM_INPUTS@ read_duplication.py -i 'input.${extension}' -o output -u ${upLimit} -q ${mapq} ]]> </command> - <inputs> <expand macro="bam_sam_param" /> <param name="upLimit" type="integer" label="Upper Limit of Plotted Duplicated Times (default=500)" value="500" help="(--up-limit)"/> <expand macro="mapq_param" /> <expand macro="rscript_output_param" /> </inputs> - <outputs> <expand macro="pdf_output_data" filename="output.DupRate_plot.pdf" label="${tool.name} on ${on_string}: plot (PDF)"/> <data format="tabular" name="outputxls" from_work_dir="output.pos.DupRate.xls" label="${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> - <tests> - <test> + <test expect_num_outputs="4"> <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" ftype="tabular"/> @@ -41,7 +34,6 @@ <output name="outputpdf" file="output.DupRate_plot.pdf" compare="sim_size" /> </test> </tests> - <help><![CDATA[ read_duplication.py +++++++++++++++++++ @@ -77,7 +69,5 @@ ]]> </help> - <expand macro="citations" /> - </tool>
--- a/read_hexamer.xml Wed Feb 22 15:06:01 2023 +0000 +++ b/read_hexamer.xml Tue Apr 09 11:24:55 2024 +0000 @@ -6,12 +6,9 @@ <import>rseqc_macros.xml</import> </macros> <expand macro="bio_tools"/> - <expand macro="requirements" /> - - <expand macro="stdio" /> - + <expand macro="requirements"/> + <expand macro="stdio"/> <version_command><![CDATA[read_hexamer.py --version]]></version_command> - <command><![CDATA[ #import re #set $input_list = [] @@ -39,51 +36,48 @@ > '${output}' ]]> </command> - <inputs> - <param name="inputs" type="data" label="Read sequences in fasta or fastq format" format="fasta,fastq,fastqsanger,fastq.gz,fastqsanger.gz" help="(--input)" multiple="true" /> - <param name="refgenome" type="data" label="Reference genome seqeunce (fasta)" format="fasta" optional="true" help="(--refgenome)" /> - <param name="refgene" type="data" label="Reference mRNA sequence (fasta)" format="fasta" optional="true" help="(--refgene)" /> + <param name="inputs" type="data" label="Read sequences in fasta or fastq format" format="fasta,fastq,fastqsanger,fastq.gz,fastqsanger.gz" help="(--input)" multiple="true"/> + <param name="refgenome" type="data" label="Reference genome seqeunce (fasta)" format="fasta" optional="true" help="(--refgenome)"/> + <param name="refgene" type="data" label="Reference mRNA sequence (fasta)" format="fasta" optional="true" help="(--refgene)"/> </inputs> - <outputs> - <data name="output" format="tabular" label="${tool.name} on ${on_string}" /> + <data name="output" format="tabular" label="${tool.name} on ${on_string}"/> </outputs> - <tests> - <test> + <test expect_num_outputs="1"> <param name="inputs" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.R1.fastq"/> <output name="output"> <assert_contents> - <has_line line="Hexamer	pairend_strandspecific_51mer_hg19_chr1_1-100000_R1_fastq" /> - <has_text text="0.002173913043478261" /> + <has_line line="Hexamer	pairend_strandspecific_51mer_hg19_chr1_1-100000_R1_fastq"/> + <has_text text="0.002173913043478261"/> </assert_contents> </output> </test> - <test> + <test expect_num_outputs="1"> <param name="inputs" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.R1.fastq.gz" ftype="fastqsanger.gz"/> <output name="output"> <assert_contents> - <has_line line="Hexamer	pairend_strandspecific_51mer_hg19_chr1_1-100000_R1_fastq_gz" /> - <has_text text="0.002173913043478261" /> + <has_line line="Hexamer	pairend_strandspecific_51mer_hg19_chr1_1-100000_R1_fastq_gz"/> + <has_text text="0.002173913043478261"/> </assert_contents> </output> </test> - <test> + <test expect_num_outputs="1"> <param name="inputs" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.R1.fastq,pairend_strandspecific_51mer_hg19_chr1_1-100000.R2.fastq"/> <output name="output"> <assert_contents> - <has_line line="Hexamer	pairend_strandspecific_51mer_hg19_chr1_1-100000_R1_fastq	pairend_strandspecific_51mer_hg19_chr1_1-100000_R2_fastq" /> - <has_text text="0.002173913043478261" /> + <has_line line="Hexamer	pairend_strandspecific_51mer_hg19_chr1_1-100000_R1_fastq	pairend_strandspecific_51mer_hg19_chr1_1-100000_R2_fastq"/> + <has_text text="0.002173913043478261"/> </assert_contents> </output> </test> - <test> + <test expect_num_outputs="1"> <param name="inputs" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.R1.fastq,pairend_strandspecific_51mer_hg19_chr1_1-100000.R1.fastq"/> <output name="output"> <assert_contents> - <has_line line="Hexamer	pairend_strandspecific_51mer_hg19_chr1_1-100000_R1_fastq	pairend_strandspecific_51mer_hg19_chr1_1-100000_R1_fastq.1" /> - <has_text text="0.002173913043478261" /> + <has_line line="Hexamer	pairend_strandspecific_51mer_hg19_chr1_1-100000_R1_fastq	pairend_strandspecific_51mer_hg19_chr1_1-100000_R1_fastq.1"/> + <has_text text="0.002173913043478261"/> </assert_contents> </output> </test> @@ -99,7 +93,6 @@ </test> --> </tests> - <help><![CDATA[ read_hexamer.py +++++++++++++++++++++ @@ -130,7 +123,5 @@ ]]> </help> - - <expand macro="citations" /> - + <expand macro="citations"/> </tool>
--- a/read_quality.xml Wed Feb 22 15:06:01 2023 +0000 +++ b/read_quality.xml Tue Apr 09 11:24:55 2024 +0000 @@ -11,11 +11,8 @@ --> <requirement type="package" version="4.2.2">r-base</requirement> </expand> - - <expand macro="stdio" /> - + <expand macro="stdio"/> <version_command><![CDATA[read_quality.py --version]]></version_command> - <command><![CDATA[ @BAM_SAM_INPUTS@ read_quality.py @@ -25,30 +22,26 @@ --mapq ${mapq} ]]> </command> - <inputs> - <expand macro="bam_sam_param" /> + <expand macro="bam_sam_param"/> <param name="reduce" type="integer" label="Ignore Phred scores less than this amount (only applies to 'boxplot', default=1000)" value="1000" help="(--reduce)"/> - <expand macro="mapq_param" /> - <expand macro="rscript_output_param" /> + <expand macro="mapq_param"/> + <expand macro="rscript_output_param"/> </inputs> - <outputs> - <data format="pdf" name="outputheatpdf" from_work_dir="output.qual.heatmap.pdf" label="${tool.name} on ${on_string} (Heatmap pdf)" /> - <data format="pdf" name="outputboxpdf" from_work_dir="output.qual.boxplot.pdf" label="${tool.name} on ${on_string} (Boxplot pdf)" /> - <expand macro="rscript_output_data" filename="output.qual.r" /> + <data format="pdf" name="outputheatpdf" from_work_dir="output.qual.heatmap.pdf" label="${tool.name} on ${on_string} (Heatmap pdf)"/> + <data format="pdf" name="outputboxpdf" from_work_dir="output.qual.boxplot.pdf" label="${tool.name} on ${on_string} (Boxplot pdf)"/> + <expand macro="rscript_output_data" filename="output.qual.r"/> </outputs> - <tests> - <test> + <test expect_num_outputs="3"> <param name="input" value="pairend_strandspecific_51mer_hg19_random.bam"/> - <param name="rscript_output" value="true" /> + <param name="rscript_output" value="true"/> <output name="outputr" file="output.qual_r"/> - <output name="outputheatpdf" file="output.qual.heatmap.pdf" compare="sim_size" /> - <output name="outputboxpdf" file="output.qual.boxplot.pdf" compare="sim_size" /> + <output name="outputheatpdf" file="output.qual.heatmap.pdf" compare="sim_size"/> + <output name="outputboxpdf" file="output.qual.boxplot.pdf" compare="sim_size"/> </test> </tests> - <help><![CDATA[ read_quality.py +++++++++++++++ @@ -92,7 +85,5 @@ ]]> </help> - - <expand macro="citations" /> - + <expand macro="citations"/> </tool>
--- a/rseqc_macros.xml Wed Feb 22 15:06:01 2023 +0000 +++ b/rseqc_macros.xml Tue Apr 09 11:24:55 2024 +0000 @@ -1,6 +1,6 @@ <macros> - <token name="@TOOL_VERSION@">5.0.1</token> - <token name="@VERSION_SUFFIX@">2</token> + <token name="@TOOL_VERSION@">5.0.3</token> + <token name="@VERSION_SUFFIX@">0</token> <token name="@GALAXY_VERSION@">20.01</token> <xml name="requirements"> <requirements> @@ -15,52 +15,41 @@ </xml> <xml name="stdio"> <stdio> - <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" /> - <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" /> + <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information"/> + <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information"/> </stdio> </xml> - <!-- Params --> <xml name="bam_param"> <param name="input" type="data" label="Input BAM file" format="bam" help="(--input-file)"/> </xml> - <xml name="bam_sam_param"> <param name="input" type="data" label="Input BAM/SAM file" format="bam,sam" help="(--input-file)"/> </xml> - <xml name="refgene_param"> <param argument="--refgene" type="data" format="bed12" label="Reference gene model" help="Reference gene model in BED fomat"/> </xml> - <xml name="mapq_param"> - <param argument="--mapq" type="integer" label="Minimum mapping quality" value="30" - help="Minimum mapping quality for an alignment to be considered as "uniquely mapped""/> + <param argument="--mapq" type="integer" label="Minimum mapping quality" value="30" help="Minimum mapping quality for an alignment to be considered as "uniquely mapped""/> </xml> - <xml name="readlength_param"> <param argument="--read-align-length" type="integer" value="" label="Alignment length" optional="false" help="Alignment length of read, usually set to the orignial read length"/> </xml> - <xml name="readnum_param"> <param argument="--read-num" type="integer" label="Number of aligned reads" value="1000000" help="Number of aligned reads with mismatches used to calculate the mismatch profile"/> </xml> - <xml name="sample_size_param"> <param argument="--sample-size" type="integer" label="Number of reads sampled" value="200000" min="1" help="Number of reads sampled from SAM/BAM file"/> </xml> - <xml name="min_intron_param"> - <param argument="--min-intron" type="integer" value="50" label="Minimum intron length (bp)" help="Default: 50" /> + <param argument="--min-intron" type="integer" value="50" label="Minimum intron length (bp)" help="Default: 50"/> </xml> - <xml name="layout_param"> <param name="layout" type="select" label="Sequencing layout" help="(--sequencing)"> <option value="SE" selected="true">Single-end</option> <option value="PE">Paired-end</option> </param> </xml> - <xml name="strand_type_param"> <conditional name="strand_type"> <param name="strand_specific" type="select" label="Strand-specific?"> @@ -69,21 +58,20 @@ <option value="single">Single-End RNA-seq</option> </param> <when value="pair"> - <param name="pair_type" type="select" display="radio" label="Pair-End Read Type (format: mapped --> parent)" help="(--strand)"> - <option value="sd" selected="true"> read1 (positive --> positive; negative --> negative), read2 (positive --> negative; negative --> positive)</option> - <option value="ds">read1 (positive --> negative; negative --> positive), read2 (positive --> positive; negative --> negative)</option> + <param name="pair_type" type="select" display="radio" label="Pair-End Read Type (format: mapped --> parent)" help="(--strand)"> + <option value="sd" selected="true"> read1 (positive --> positive; negative --> negative), read2 (positive --> negative; negative --> positive)</option> + <option value="ds">read1 (positive --> negative; negative --> positive), read2 (positive --> positive; negative --> negative)</option> </param> </when> <when value="single"> - <param name="single_type" type="select" display="radio" label="Single-End Read Type (format: mapped --> parent)" help="(--strand)"> - <option value="s" selected="true">positive --> positive; negative --> negative</option> - <option value="d">positive --> negative; negative --> positive</option> + <param name="single_type" type="select" display="radio" label="Single-End Read Type (format: mapped --> parent)" help="(--strand)"> + <option value="s" selected="true">positive --> positive; negative --> negative</option> + <option value="d">positive --> negative; negative --> positive</option> </param> </when> - <when value="none"></when> + <when value="none"/> </conditional> </xml> - <xml name="multihits_param"> <conditional name="multihits_type"> <param name="multihits_type_selector" type="select" label="Reads with multiple hits" help="(--skip-multi-hits)"> @@ -91,34 +79,26 @@ <option value="skip_multihits">Skip Multiple Hit Reads/Only Use Uniquely Mapped Reads</option> </param> <when value="skip_multihits"> - <expand macro="mapq_param" /> + <expand macro="mapq_param"/> </when> - <when value="use_multihits" /> + <when value="use_multihits"/> </conditional> </xml> - <xml name="rscript_output_param"> - <param name="rscript_output" type="boolean" value="false" label="Output R-Script" - help="Output the R-Script used to generate the plots" /> + <param name="rscript_output" type="boolean" value="false" label="Output R-Script" help="Output the R-Script used to generate the plots"/> </xml> - - <!-- Output --> - <xml name="pdf_output_data" token_filename="output.pdf" token_label="${tool.name} on ${on_string}: PDF"> - <data format="pdf" name="outputpdf" from_work_dir="@FILENAME@" label="@LABEL@" /> + <data format="pdf" name="outputpdf" from_work_dir="@FILENAME@" label="@LABEL@"/> </xml> - <xml name="xls_output_data" token_filename="output.xls" token_label="${tool.name} on ${on_string}: XLS"> - <data format="tabular" name="outputxls" from_work_dir="@FILENAME@" label="@LABEL@" /> + <data format="tabular" name="outputxls" from_work_dir="@FILENAME@" label="@LABEL@"/> </xml> - <xml name="rscript_output_data" token_filename="output.r" token_label="${tool.name} on ${on_string}: Rscript"> <data format="txt" name="outputr" from_work_dir="@FILENAME@" label="@LABEL@"> <filter>rscript_output</filter> </data> </xml> - <!-- Command --> <token name="@MULTIHITS@"><![CDATA[ #if str($multihits_type.multihits_type_selector) == "skip_multihits" @@ -126,7 +106,6 @@ --mapq=${multihits_type.mapq} #end if ]]></token> - <token name="@BAM_SAM_INPUTS@"><![CDATA[ #set $extension = str($input.ext) ln -s -f '${input}' 'input.${extension}' && @@ -134,7 +113,6 @@ ln -s -f '${input.metadata.bam_index}' 'input.bam.bai' && #end if ]]></token> - <token name="@ABOUT@"> ----- @@ -158,7 +136,6 @@ </token> - <xml name="citations"> <citations> <citation type="doi">10.1093/bioinformatics/bts356</citation>
--- a/tin.xml Wed Feb 22 15:06:01 2023 +0000 +++ b/tin.xml Tue Apr 09 11:24:55 2024 +0000 @@ -6,13 +6,9 @@ <import>rseqc_macros.xml</import> </macros> <expand macro="bio_tools"/> - - <expand macro="requirements" /> - - <expand macro="stdio" /> - + <expand macro="requirements"/> + <expand macro="stdio"/> <version_command><![CDATA[tin.py --version]]></version_command> - <!-- Generate output files here because tin.py removes all instances of "bam" in the filename --> <command><![CDATA[ @@ -34,28 +30,17 @@ && mv *tin.xls tin.xls ]]> </command> - <inputs> <param name="input" type="data" format="bam" multiple="true" label="Input BAM file" help="(--input-file)"/> - <expand macro="refgene_param" /> - <param name="minCov" type="integer" value="10" label="Minimum coverage (default=10)" - help="Minimum number of reads mapped to a transcript (--minCov)." /> - <param name="samplesize" type="integer" value="100" label="Sample size (default=100)" - help="Number of equal-spaced nucleotide positions picked from mRNA. - Note: if this number is larger than the length of mRNA (L), it will - be halved until is's smaller than L. (--sample-size)." /> - <param name="subtractbackground" type="boolean" value="false" falsevalue="" - truevalue="--subtract-background" label="Subtract background noise - (default=No)" help="Subtract background noise (estimated from - intronic reads). Only use this option if there are substantial - intronic reads (--subtract-background)." /> + <expand macro="refgene_param"/> + <param name="minCov" type="integer" value="10" label="Minimum coverage (default=10)" help="Minimum number of reads mapped to a transcript (--minCov)."/> + <param name="samplesize" type="integer" value="100" label="Sample size (default=100)" help="Number of equal-spaced nucleotide positions picked from mRNA. Note: if this number is larger than the length of mRNA (L), it will be halved until is's smaller than L. (--sample-size)."/> + <param name="subtractbackground" type="boolean" value="false" falsevalue="" truevalue="--subtract-background" label="Subtract background noise (default=No)" help="Subtract background noise (estimated from intronic reads). Only use this option if there are substantial intronic reads (--subtract-background)."/> </inputs> - <outputs> - <data name="outputsummary" format="tabular" from_work_dir="summary.tab" label="TIN on ${on_string} (summary)" /> - <data name="outputxls" format="tabular" from_work_dir="tin.xls" label="TIN on ${on_string} (tin)" /> + <data name="outputsummary" format="tabular" from_work_dir="summary.tab" label="TIN on ${on_string} (summary)"/> + <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 --> <tests> <test expect_num_outputs="2"> @@ -65,7 +50,6 @@ <output name="outputxls" file="output.tin.xls" ftype="tabular"/> </test> </tests> - <help><![CDATA[ ## tin.py @@ -149,7 +133,5 @@ ]]> </help> - - <expand macro="citations" /> - + <expand macro="citations"/> </tool>