| Previous changeset 59:dbedfc5f5a3c (2021-12-18) Next changeset 61:5968573462fa (2022-12-10) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 1dfe55ca83685cadb0ce8f6ebbd8c13232376d1d |
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modified:
FPKM_count.xml RNA_fragment_size.xml RPKM_saturation.xml bam2wig.xml bam_stat.xml clipping_profile.xml deletion_profile.xml geneBody_coverage.xml geneBody_coverage2.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 test-data/output.FPKM.xls test-data/output.GC.xls test-data/output.GC_plot.pdf test-data/output.GC_plot_r test-data/output.NVC.xls test-data/output.NVC_plot.pdf test-data/output.geneBodyCoverage2.curves.pdf test-data/output.geneBodyCoverage2.txt test-data/output.geneBodyCoverage2_r test-data/output.inner_distance_plot.pdf test-data/output.inner_distance_plot_r test-data/output.junction.xls test-data/output.junction_plot_r test-data/output.splice_events.pdf test-data/output.splice_junction.pdf test-data/output.tin.xls test-data/testwig.Forward.wig test-data/testwig.Reverse.wig test-data/testwig.wig test-data/testwig_wigsum100.wig tin.xml |
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added:
test-data/summary.tin.txt |
| b |
| diff -r dbedfc5f5a3c -r 1421603cc95b FPKM_count.xml --- a/FPKM_count.xml Sat Dec 18 19:41:19 2021 +0000 +++ b/FPKM_count.xml Sat Nov 26 15:19:14 2022 +0000 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="rseqc_FPKM_count" name="FPKM Count" version="@TOOL_VERSION@.1"> +<tool id="rseqc_FPKM_count" name="FPKM Count" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@"> <description>calculates raw read count, FPM, and FPKM for each gene</description> <expand macro="bio_tools"/> <macros> @@ -12,9 +12,8 @@ <version_command><![CDATA[FPKM_count.py --version]]></version_command> <command><![CDATA[ - ln -sf '${input}' 'local_input.bam' && - ln -sf '${input.metadata.bam_index}' 'local_input.bam.bai' && - FPKM_count.py -i 'local_input.bam' -o output -r '${refgene}' + @BAM_SAM_INPUTS@ + FPKM_count.py -i 'input.${extension}' -o output -r '${refgene}' #if str($strand_type.strand_specific) == "pair" -d |
| b |
| diff -r dbedfc5f5a3c -r 1421603cc95b RNA_fragment_size.xml --- a/RNA_fragment_size.xml Sat Dec 18 19:41:19 2021 +0000 +++ b/RNA_fragment_size.xml Sat Nov 26 15:19:14 2022 +0000 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="rseqc_RNA_fragment_size" name="RNA fragment size" version="@TOOL_VERSION@.1"> +<tool id="rseqc_RNA_fragment_size" name="RNA fragment size" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@"> <description> calculates the fragment size for each gene/transcript </description> @@ -14,9 +14,8 @@ <version_command><![CDATA[RNA_fragment_size.py --version]]></version_command> <command><![CDATA[ - ln -sf '${input}' 'input.bam' && - ln -sf '$input.metadata.bam_index' 'input.bam.bai' && - RNA_fragment_size.py -i 'input.bam' --refgene='${refgene}' --mapq=${mapq} --frag-num=${fragnum} > '${output}' + @BAM_SAM_INPUTS@ + RNA_fragment_size.py -i 'input.${extension}' --refgene='${refgene}' --mapq=${mapq} --frag-num=${fragnum} > '${output}' ]]> </command> |
| b |
| diff -r dbedfc5f5a3c -r 1421603cc95b RPKM_saturation.xml --- a/RPKM_saturation.xml Sat Dec 18 19:41:19 2021 +0000 +++ b/RPKM_saturation.xml Sat Nov 26 15:19:14 2022 +0000 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="rseqc_RPKM_saturation" name="RPKM Saturation" version="@TOOL_VERSION@.2"> +<tool id="rseqc_RPKM_saturation" name="RPKM Saturation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@"> <description>calculates raw count and RPKM values for transcript at exon, intron, and mRNA level</description> <expand macro="bio_tools"/> <macros> @@ -12,7 +12,8 @@ <version_command><![CDATA[RPKM_saturation.py --version]]></version_command> <command><![CDATA[ - RPKM_saturation.py -i '${input}' -o output -r '${refgene}' + @BAM_SAM_INPUTS@ + RPKM_saturation.py -i 'input.${extension}' -o output -r '${refgene}' #if str($strand_type.strand_specific) == "pair" -d @@ -37,7 +38,7 @@ ]]></command> <inputs> - <expand macro="bam_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)"/> |
| b |
| diff -r dbedfc5f5a3c -r 1421603cc95b bam2wig.xml --- a/bam2wig.xml Sat Dec 18 19:41:19 2021 +0000 +++ b/bam2wig.xml Sat Nov 26 15:19:14 2022 +0000 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="rseqc_bam2wig" name="BAM to Wiggle" version="@TOOL_VERSION@"> +<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 </description> @@ -14,9 +14,8 @@ <version_command><![CDATA[bam2wig.py --version]]></version_command> <command><![CDATA[ - ln -sf '${input}' 'input.bam' && - ln -sf '${input.metadata.bam_index}' 'input.bam.bai' && - bam2wig.py -i 'input.bam' -s '${chromsize}' -o outfile + @BAM_SAM_INPUTS@ + bam2wig.py -i 'input.${extension}' -s '${chromsize}' -o outfile #if str($strand_type.strand_specific) == "pair" -d |
| b |
| diff -r dbedfc5f5a3c -r 1421603cc95b bam_stat.xml --- a/bam_stat.xml Sat Dec 18 19:41:19 2021 +0000 +++ b/bam_stat.xml Sat Nov 26 15:19:14 2022 +0000 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="rseqc_bam_stat" name="BAM/SAM Mapping Stats" version="@TOOL_VERSION@"> +<tool id="rseqc_bam_stat" name="BAM/SAM Mapping Stats" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@"> <description> reads mapping statistics for a provided BAM or SAM file. </description> @@ -14,12 +14,13 @@ <version_command><![CDATA[bam_stat.py --version]]></version_command> <command><![CDATA[ - bam_stat.py -i '${input}' -q ${mapq} > '${output}' + @BAM_SAM_INPUTS@ + bam_stat.py -i 'input.${extension}' -q ${mapq} > '${output}' ]]> </command> <inputs> - <expand macro="bam_param" /> + <expand macro="bam_sam_param" /> <expand macro="mapq_param" /> </inputs> |
| b |
| diff -r dbedfc5f5a3c -r 1421603cc95b clipping_profile.xml --- a/clipping_profile.xml Sat Dec 18 19:41:19 2021 +0000 +++ b/clipping_profile.xml Sat Nov 26 15:19:14 2022 +0000 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="rseqc_clipping_profile" name="Clipping Profile" version="@TOOL_VERSION@"> +<tool id="rseqc_clipping_profile" name="Clipping Profile" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@"> <description> estimates clipping profile of RNA-seq reads from BAM or SAM file </description> @@ -14,7 +14,8 @@ <version_command><![CDATA[clipping_profile.py --version]]></version_command> <command><![CDATA[ - clipping_profile.py -i '${input}' -o output -q ${mapq} -s "${layout}" + @BAM_SAM_INPUTS@ + clipping_profile.py -i 'input.${extension}' -o output -q ${mapq} -s "${layout}" ]]> </command> |
| b |
| diff -r dbedfc5f5a3c -r 1421603cc95b deletion_profile.xml --- a/deletion_profile.xml Sat Dec 18 19:41:19 2021 +0000 +++ b/deletion_profile.xml Sat Nov 26 15:19:14 2022 +0000 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="rseqc_deletion_profile" name="Deletion Profile" version="@TOOL_VERSION@"> +<tool id="rseqc_deletion_profile" name="Deletion Profile" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@"> <description> calculates the distributions of deleted nucleotides across reads </description> @@ -14,7 +14,8 @@ <version_command><![CDATA[deletion_profile.py --version]]></version_command> <command><![CDATA[ - deletion_profile.py -i '${input}' -o output -l ${readlength} -n ${readnum} -q ${mapq} + @BAM_SAM_INPUTS@ + deletion_profile.py -i 'input.${extension}' -o output -l ${read_align_length} -n ${read_num} -q ${mapq} ]]> </command> @@ -35,7 +36,7 @@ <tests> <test> <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" /> - <param name="readlength" value="101" /> + <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" /> |
| b |
| diff -r dbedfc5f5a3c -r 1421603cc95b geneBody_coverage.xml --- a/geneBody_coverage.xml Sat Dec 18 19:41:19 2021 +0000 +++ b/geneBody_coverage.xml Sat Nov 26 15:19:14 2022 +0000 |
| b |
| @@ -1,5 +1,5 @@ -<tool id="rseqc_geneBody_coverage" name="Gene Body Coverage (BAM)" version="@TOOL_VERSION@.3"> - <description>Read coverage over gene body</description> +<tool id="rseqc_geneBody_coverage" name="Gene Body Coverage (BAM)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@"> + <description>read coverage over gene body</description> <expand macro="bio_tools"/> <macros> <import>rseqc_macros.xml</import> |
| b |
| diff -r dbedfc5f5a3c -r 1421603cc95b geneBody_coverage2.xml --- a/geneBody_coverage2.xml Sat Dec 18 19:41:19 2021 +0000 +++ b/geneBody_coverage2.xml Sat Nov 26 15:19:14 2022 +0000 |
| b |
| @@ -1,7 +1,5 @@ -<tool id="rseqc_geneBody_coverage2" name="Gene Body Coverage (Bigwig)" version="@TOOL_VERSION@.2"> - <description> - Read coverage over gene body - </description> +<tool id="rseqc_geneBody_coverage2" name="Gene Body Coverage (Bigwig)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@"> + <description>read coverage over gene body</description> <expand macro="bio_tools"/> <macros> <import>rseqc_macros.xml</import> |
| b |
| diff -r dbedfc5f5a3c -r 1421603cc95b infer_experiment.xml --- a/infer_experiment.xml Sat Dec 18 19:41:19 2021 +0000 +++ b/infer_experiment.xml Sat Nov 26 15:19:14 2022 +0000 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="rseqc_infer_experiment" name="Infer Experiment" version="@TOOL_VERSION@.1"> +<tool id="rseqc_infer_experiment" name="Infer Experiment" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@"> <description>speculates how RNA-seq were configured</description> <expand macro="bio_tools"/> <macros> @@ -12,7 +12,8 @@ <version_command><![CDATA[infer_experiment.py --version]]></version_command> <command><![CDATA[ - infer_experiment.py -i '${input}' -r '${refgene}' + @BAM_SAM_INPUTS@ + infer_experiment.py -i 'input.${extension}' -r '${refgene}' --sample-size ${sample_size} --mapq ${mapq} > '${output}' @@ -27,7 +28,7 @@ </inputs> <outputs> - <data format="txt" name="output" /> + <data format="txt" name="output" label="${tool.name} on ${on_string}: RNA-seq experiment configuration" /> </outputs> <tests> |
| b |
| diff -r dbedfc5f5a3c -r 1421603cc95b inner_distance.xml --- a/inner_distance.xml Sat Dec 18 19:41:19 2021 +0000 +++ b/inner_distance.xml Sat Nov 26 15:19:14 2022 +0000 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="rseqc_inner_distance" name="Inner Distance" version="@TOOL_VERSION@.1"> +<tool id="rseqc_inner_distance" name="Inner Distance" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@"> <description>calculate the inner distance (or insert size) between two paired RNA reads</description> <expand macro="bio_tools"/> <macros> @@ -12,7 +12,8 @@ <version_command><![CDATA[inner_distance.py --version]]></version_command> <command><![CDATA[ - inner_distance.py -i '${input}' -o output -r '${refgene}' + @BAM_SAM_INPUTS@ + inner_distance.py -i 'input.${extension}' -o output -r '${refgene}' --sample-size ${sample_size} --lower-bound ${lowerBound} --upper-bound ${upperBound} |
| b |
| diff -r dbedfc5f5a3c -r 1421603cc95b insertion_profile.xml --- a/insertion_profile.xml Sat Dec 18 19:41:19 2021 +0000 +++ b/insertion_profile.xml Sat Nov 26 15:19:14 2022 +0000 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="rseqc_insertion_profile" name="Insertion Profile" version="@TOOL_VERSION@"> +<tool id="rseqc_insertion_profile" name="Insertion Profile" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@"> <description> calculates the distribution of inserted nucleotides across reads </description> @@ -14,12 +14,13 @@ <version_command><![CDATA[insertion_profile.py --version]]></version_command> <command><![CDATA[ - insertion_profile.py -i '${input}' -o output -q ${mapq} -s "${layout}" + @BAM_SAM_INPUTS@ + insertion_profile.py -i 'input.${extension}' -o output -q ${mapq} -s "${layout}" ]]> </command> <inputs> - <expand macro="bam_param" /> + <expand macro="bam_sam_param" /> <expand macro="mapq_param" /> <expand macro="layout_param" /> <expand macro="rscript_output_param" /> |
| b |
| diff -r dbedfc5f5a3c -r 1421603cc95b junction_annotation.xml --- a/junction_annotation.xml Sat Dec 18 19:41:19 2021 +0000 +++ b/junction_annotation.xml Sat Nov 26 15:19:14 2022 +0000 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="rseqc_junction_annotation" name="Junction Annotation" version="@TOOL_VERSION@.1"> +<tool id="rseqc_junction_annotation" name="Junction Annotation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@"> <description>compares detected splice junctions to reference gene model</description> <expand macro="bio_tools"/> <macros> @@ -10,7 +10,7 @@ Required due to conda solver bug: https://github.com/conda/conda/issues/6269 See: https://github.com/galaxyproject/tools-iuc/pull/1578 for more info --> - <requirement type="package" version="3.4.1">r-base</requirement> + <requirement type="package" version="4.2.2">r-base</requirement> </expand> <expand macro="stdio" /> @@ -18,8 +18,9 @@ <version_command><![CDATA[junction_annotation.py --version]]></version_command> <command><![CDATA[ + @BAM_SAM_INPUTS@ junction_annotation.py - --input-file '${input}' + --input-file 'input.${extension}' --refgene '${refgene}' --out-prefix output --min-intron ${min_intron} |
| b |
| diff -r dbedfc5f5a3c -r 1421603cc95b junction_saturation.xml --- a/junction_saturation.xml Sat Dec 18 19:41:19 2021 +0000 +++ b/junction_saturation.xml Sat Nov 26 15:19:14 2022 +0000 |
| [ |
| @@ -1,19 +1,16 @@ -<tool id="rseqc_junction_saturation" name="Junction Saturation" version="@TOOL_VERSION@.1"> +<tool id="rseqc_junction_saturation" name="Junction Saturation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@"> <description>detects splice junctions from each subset and compares them to reference gene model</description> <expand macro="bio_tools"/> <macros> <import>rseqc_macros.xml</import> </macros> - <expand macro="requirements" /> - <expand macro="stdio" /> - <version_command><![CDATA[junction_saturation.py --version]]></version_command> - <command><![CDATA[ + @BAM_SAM_INPUTS@ junction_saturation.py - --input-file '${input}' + --input-file 'input.${extension}' --refgene '${refgene}' --out-prefix output --min-intron ${min_intron} |
| b |
| diff -r dbedfc5f5a3c -r 1421603cc95b mismatch_profile.xml --- a/mismatch_profile.xml Sat Dec 18 19:41:19 2021 +0000 +++ b/mismatch_profile.xml Sat Nov 26 15:19:14 2022 +0000 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="rseqc_mismatch_profile" name="Mismatch Profile" version="@TOOL_VERSION@"> +<tool id="rseqc_mismatch_profile" name="Mismatch Profile" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@"> <description> calculates the distribution of mismatches across reads </description> @@ -14,7 +14,8 @@ <version_command><![CDATA[mismatch_profile.py --version]]></version_command> <command><![CDATA[ - mismatch_profile.py -i '${input}' -o output -l ${readlength} -n ${readnum} -q ${mapq} + @BAM_SAM_INPUTS@ + mismatch_profile.py -i 'input.${extension}' -o output -l ${read_align_length} -n ${read_num} -q ${mapq} ]]> </command> @@ -35,7 +36,7 @@ <tests> <test> <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/> - <param name="readlength" value="101" /> + <param name="read_align_length" value="101" /> <param name="rscript_output" value="true" /> <output name="outputpdf" file="output.mismatch_profile.pdf" compare="sim_size" /> <output name="outputxls" file="output.mismatch_profile.xls"/> |
| b |
| diff -r dbedfc5f5a3c -r 1421603cc95b read_GC.xml --- a/read_GC.xml Sat Dec 18 19:41:19 2021 +0000 +++ b/read_GC.xml Sat Nov 26 15:19:14 2022 +0000 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="rseqc_read_GC" name="Read GC" version="@TOOL_VERSION@"> +<tool id="rseqc_read_GC" name="Read GC" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@"> <description>determines GC% and read count</description> <expand macro="bio_tools"/> <macros> @@ -12,8 +12,9 @@ <version_command><![CDATA[read_GC.py --version]]></version_command> <command><![CDATA[ + @BAM_SAM_INPUTS@ read_GC.py - --input-file '${input}' + --input-file 'input.${extension}' --out-prefix output --mapq ${mapq} ]]> |
| b |
| diff -r dbedfc5f5a3c -r 1421603cc95b read_NVC.xml --- a/read_NVC.xml Sat Dec 18 19:41:19 2021 +0000 +++ b/read_NVC.xml Sat Nov 26 15:19:14 2022 +0000 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="rseqc_read_NVC" name="Read NVC" version="@TOOL_VERSION@"> +<tool id="rseqc_read_NVC" name="Read NVC" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@"> <description>to check the nucleotide composition bias</description> <expand macro="bio_tools"/> <macros> @@ -12,8 +12,9 @@ <version_command><![CDATA[read_NVC.py --version]]></version_command> <command><![CDATA[ + @BAM_SAM_INPUTS@ read_NVC.py - --input-file '${input}' + --input-file 'input.${extension}' --out-prefix output ${nx} --mapq ${mapq} |
| b |
| diff -r dbedfc5f5a3c -r 1421603cc95b read_distribution.xml --- a/read_distribution.xml Sat Dec 18 19:41:19 2021 +0000 +++ b/read_distribution.xml Sat Nov 26 15:19:14 2022 +0000 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="rseqc_read_distribution" name="Read Distribution" version="@TOOL_VERSION@.1"> +<tool id="rseqc_read_distribution" name="Read Distribution" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@"> <description>calculates how mapped reads were distributed over genome feature</description> <expand macro="bio_tools"/> <macros> @@ -12,7 +12,8 @@ <version_command><![CDATA[read_distribution.py --version]]></version_command> <command><![CDATA[ - read_distribution.py -i '${input}' -r '${refgene}' > '${output}' + @BAM_SAM_INPUTS@ + read_distribution.py -i 'input.${extension}' -r '${refgene}' > '${output}' ]]> </command> |
| b |
| diff -r dbedfc5f5a3c -r 1421603cc95b read_duplication.xml --- a/read_duplication.xml Sat Dec 18 19:41:19 2021 +0000 +++ b/read_duplication.xml Sat Nov 26 15:19:14 2022 +0000 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="rseqc_read_duplication" name="Read Duplication" version="@TOOL_VERSION@"> +<tool id="rseqc_read_duplication" name="Read Duplication" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@"> <description>determines reads duplication rate with sequence-based and mapping-based strategies</description> <expand macro="bio_tools"/> <macros> @@ -12,7 +12,8 @@ <version_command><![CDATA[read_duplication.py --version]]></version_command> <command><![CDATA[ - read_duplication.py -i '${input}' -o output -u ${upLimit} -q ${mapq} + @BAM_SAM_INPUTS@ + read_duplication.py -i 'input.${extension}' -o output -u ${upLimit} -q ${mapq} ]]> </command> |
| b |
| diff -r dbedfc5f5a3c -r 1421603cc95b read_hexamer.xml --- a/read_hexamer.xml Sat Dec 18 19:41:19 2021 +0000 +++ b/read_hexamer.xml Sat Nov 26 15:19:14 2022 +0000 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="rseqc_read_hexamer" name="Hexamer frequency" version="@TOOL_VERSION@"> +<tool id="rseqc_read_hexamer" name="Hexamer frequency" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@"> <description> calculates hexamer (6mer) frequency for reads, genomes, and mRNA sequences </description> @@ -57,7 +57,7 @@ <output name="output"> <assert_contents> <has_line line="Hexamer	pairend_strandspecific_51mer_hg19_chr1_1-100000_R1_fastq" /> - <has_line line="AAAAAA	0.00217391304348" /> + <has_text text="0.002173913043478261" /> </assert_contents> </output> </test> @@ -66,7 +66,7 @@ <output name="output"> <assert_contents> <has_line line="Hexamer	pairend_strandspecific_51mer_hg19_chr1_1-100000_R1_fastq_gz" /> - <has_line line="AAAAAA	0.00217391304348" /> + <has_text text="0.002173913043478261" /> </assert_contents> </output> </test> @@ -75,7 +75,7 @@ <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_line line="AAAAAA	0.00217391304348	0.00534759358289" /> + <has_text text="0.002173913043478261" /> </assert_contents> </output> </test> @@ -84,7 +84,7 @@ <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_line line="AAAAAA	0.00217391304348	0.00217391304348" /> + <has_text text="0.002173913043478261" /> </assert_contents> </output> </test> |
| b |
| diff -r dbedfc5f5a3c -r 1421603cc95b read_quality.xml --- a/read_quality.xml Sat Dec 18 19:41:19 2021 +0000 +++ b/read_quality.xml Sat Nov 26 15:19:14 2022 +0000 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="rseqc_read_quality" name="Read Quality" version="@TOOL_VERSION@"> +<tool id="rseqc_read_quality" name="Read Quality" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@"> <description>determines Phred quality score</description> <expand macro="bio_tools"/> <macros> @@ -10,7 +10,7 @@ Required due to conda solver bug: https://github.com/conda/conda/issues/6269 See: https://github.com/galaxyproject/tools-iuc/pull/1578 for more info --> - <requirement type="package" version="3.4.1">r-base</requirement> + <requirement type="package" version="4.2.2">r-base</requirement> </expand> <expand macro="stdio" /> @@ -18,8 +18,9 @@ <version_command><![CDATA[read_quality.py --version]]></version_command> <command><![CDATA[ + @BAM_SAM_INPUTS@ read_quality.py - --input-file '${input}' + --input-file 'input.${extension}' --out-prefix output -r ${reduce} --mapq ${mapq} |
| b |
| diff -r dbedfc5f5a3c -r 1421603cc95b rseqc_macros.xml --- a/rseqc_macros.xml Sat Dec 18 19:41:19 2021 +0000 +++ b/rseqc_macros.xml Sat Nov 26 15:19:14 2022 +0000 |
| [ |
| @@ -1,10 +1,10 @@ <macros> - - <token name="@TOOL_VERSION@">2.6.4</token> - + <token name="@TOOL_VERSION@">5.0.1</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@GALAXY_VERSION@">20.01</token> <xml name="requirements"> <requirements> - <requirement type="package" version="2.6.4">rseqc</requirement> + <requirement type="package" version="@TOOL_VERSION@">rseqc</requirement> <yield/> </requirements> </xml> @@ -22,35 +22,36 @@ <!-- Params --> <xml name="bam_param"> - <param name="input" type="data" label="Input .bam file" format="bam" help="(--input-file)"/> + <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)"/> + <param name="input" type="data" label="Input BAM/SAM file" format="bam,sam" help="(--input-file)"/> </xml> <xml name="refgene_param"> - <param name="refgene" type="data" format="bed12" label="Reference gene model" help="(--refgene)"/> + <param argument="--refgene" type="data" format="bed12" label="Reference gene model" help="Reference gene model in BED fomat"/> </xml> <xml name="mapq_param"> - <param name="mapq" type="integer" label="Minimum mapping quality" value="30" help="Minimum mapping quality for an alignment to be considered as "uniquely mapped" (--mapq)"/> + <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 name="readlength" type="integer" value="" label="Alignment length" optional="false" help="Alignment length of read, usually set to the orignial read length (--read-align-length)"/> + <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 name="readnum" type="integer" label="Number of aligned reads" value="1000000" help="Number of aligned reads with mismatches used to calculate the mismatch profile (--read-num)"/> + <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 name="sample_size" type="integer" label="Number of reads sampled from SAM/BAM file (default = 200000)" value="200000" min="1" help="(--sample-size)"/> + <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 name="min_intron" type="integer" value="50" label="Minimum intron length (bp, default=50)" help="(--min-intron)" /> + <param argument="--min-intron" type="integer" value="50" label="Minimum intron length (bp)" help="Default: 50" /> </xml> <xml name="layout_param"> @@ -119,14 +120,20 @@ </xml> <!-- Command --> - <token name="@MULTIHITS@"> -<![CDATA[ -#if str($multihits_type.multihits_type_selector) == "skip_multihits" - --skip-multi-hits - --mapq=${multihits_type.mapq} -#end if -]]> - </token> + <token name="@MULTIHITS@"><![CDATA[ + #if str($multihits_type.multihits_type_selector) == "skip_multihits" + --skip-multi-hits + --mapq=${multihits_type.mapq} + #end if + ]]></token> + + <token name="@BAM_SAM_INPUTS@"><![CDATA[ + #set $extension = str($input.ext) + ln -s -f '${input}' 'input.${extension}' && + #if $extension == 'bam' + ln -s -f '${input.metadata.bam_index}' 'input.bam.bai' && + #end if + ]]></token> <token name="@ABOUT@"> |
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| diff -r dbedfc5f5a3c -r 1421603cc95b test-data/output.FPKM.xls --- a/test-data/output.FPKM.xls Sat Dec 18 19:41:19 2021 +0000 +++ b/test-data/output.FPKM.xls Sat Nov 26 15:19:14 2022 +0000 |
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| @@ -1,6 +1,6 @@ #chrom st end accession mRNA_size gene_strand Frag_count FPM FPKM -chr1 11873 14409 NR_046018 1652.0 + 1.0 50000.0 30266.3438257 -chr1 14361 29370 NR_024540 1769.0 - 2.0 100000.0 56529.1124929 +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 |
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| diff -r dbedfc5f5a3c -r 1421603cc95b test-data/output.GC.xls --- a/test-data/output.GC.xls Sat Dec 18 19:41:19 2021 +0000 +++ b/test-data/output.GC.xls Sat Nov 26 15:19:14 2022 +0000 |
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| @@ -1,19 +1,19 @@ GC% read_count +56.86 7 +68.63 1 60.78 3 -41.18 3 -47.06 5 -56.86 7 -29.41 1 27.45 2 37.25 2 +58.82 1 78.43 1 -58.82 1 50.98 3 +43.14 2 49.02 2 +52.94 3 62.75 1 -68.63 1 +47.06 5 +41.18 3 54.90 1 -52.94 3 +29.41 1 +39.22 1 35.29 1 -43.14 2 -39.22 1 |
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| diff -r dbedfc5f5a3c -r 1421603cc95b test-data/output.GC_plot.pdf |
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| Binary file test-data/output.GC_plot.pdf has changed |
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| diff -r dbedfc5f5a3c -r 1421603cc95b test-data/output.GC_plot_r --- a/test-data/output.GC_plot_r Sat Dec 18 19:41:19 2021 +0000 +++ b/test-data/output.GC_plot_r Sat Nov 26 15:19:14 2022 +0000 |
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| @@ -1,4 +1,4 @@ pdf("output.GC_plot.pdf") -gc=rep(c(60.78,41.18,47.06,56.86,29.41,27.45,37.25,78.43,58.82,50.98,49.02,62.75,68.63,54.90,52.94,35.29,43.14,39.22),times=c(3,3,5,7,1,2,2,1,1,3,2,1,1,1,3,1,2,1)) +gc=rep(c(56.86,68.63,60.78,27.45,37.25,58.82,78.43,50.98,43.14,49.02,52.94,62.75,47.06,41.18,54.90,29.41,39.22,35.29),times=c(7,1,3,2,2,1,1,3,2,2,3,1,5,3,1,1,1,1)) hist(gc,probability=T,breaks=100,xlab="GC content (%)",ylab="Density of Reads",border="blue",main="") dev.off() |
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| diff -r dbedfc5f5a3c -r 1421603cc95b test-data/output.NVC.xls --- a/test-data/output.NVC.xls Sat Dec 18 19:41:19 2021 +0000 +++ b/test-data/output.NVC.xls Sat Nov 26 15:19:14 2022 +0000 |
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| @@ -1,52 +1,52 @@ Position A C G T N X -0 5 7 18 10 0 0 -1 6 7 15 8 4 0 -2 5 9 18 5 3 0 -3 11 9 14 4 2 0 -4 5 9 12 14 0 0 -5 4 11 19 6 0 0 -6 11 7 12 10 0 0 -7 9 8 12 9 2 0 -8 12 9 11 8 0 0 -9 8 9 8 10 5 0 -10 9 8 9 14 0 0 -11 9 6 11 14 0 0 -12 14 8 12 6 0 0 -13 10 6 9 15 0 0 -14 9 9 7 15 0 0 -15 10 10 9 9 2 0 -16 8 4 6 14 8 0 -17 9 9 10 9 3 0 -18 7 5 11 12 5 0 -19 12 8 4 10 6 0 -20 10 6 9 15 0 0 -21 9 9 15 7 0 0 -22 14 6 11 9 0 0 -23 13 11 11 5 0 0 -24 12 8 7 10 3 0 -25 9 13 4 8 6 0 -26 11 16 7 6 0 0 -27 11 8 13 8 0 0 -28 13 6 9 12 0 0 -29 9 9 12 10 0 0 -30 8 6 15 11 0 0 -31 7 9 11 13 0 0 -32 7 8 14 11 0 0 -33 11 11 10 8 0 0 -34 6 12 13 9 0 0 -35 8 17 11 4 0 0 -36 9 8 7 16 0 0 -37 11 9 12 8 0 0 -38 8 9 10 13 0 0 -39 8 12 11 9 0 0 -40 12 9 10 9 0 0 -41 9 13 11 7 0 0 -42 10 12 9 9 0 0 -43 7 13 11 9 0 0 -44 10 12 6 12 0 0 -45 10 10 9 11 0 0 -46 7 10 10 13 0 0 -47 9 9 12 10 0 0 -48 10 6 14 10 0 0 -49 8 10 13 9 0 0 -50 7 8 9 16 0 0 +0 5 7 18 10 0 0 +1 6 7 15 8 4 0 +2 5 9 18 5 3 0 +3 11 9 14 4 2 0 +4 5 9 12 14 0 0 +5 4 11 19 6 0 0 +6 11 7 12 10 0 0 +7 9 8 12 9 2 0 +8 12 9 11 8 0 0 +9 8 9 8 10 5 0 +10 9 8 9 14 0 0 +11 9 6 11 14 0 0 +12 14 8 12 6 0 0 +13 10 6 9 15 0 0 +14 9 9 7 15 0 0 +15 10 10 9 9 2 0 +16 8 4 6 14 8 0 +17 9 9 10 9 3 0 +18 7 5 11 12 5 0 +19 12 8 4 10 6 0 +20 10 6 9 15 0 0 +21 9 9 15 7 0 0 +22 14 6 11 9 0 0 +23 13 11 11 5 0 0 +24 12 8 7 10 3 0 +25 9 13 4 8 6 0 +26 11 16 7 6 0 0 +27 11 8 13 8 0 0 +28 13 6 9 12 0 0 +29 9 9 12 10 0 0 +30 8 6 15 11 0 0 +31 7 9 11 13 0 0 +32 7 8 14 11 0 0 +33 11 11 10 8 0 0 +34 6 12 13 9 0 0 +35 8 17 11 4 0 0 +36 9 8 7 16 0 0 +37 11 9 12 8 0 0 +38 8 9 10 13 0 0 +39 8 12 11 9 0 0 +40 12 9 10 9 0 0 +41 9 13 11 7 0 0 +42 10 12 9 9 0 0 +43 7 13 11 9 0 0 +44 10 12 6 12 0 0 +45 10 10 9 11 0 0 +46 7 10 10 13 0 0 +47 9 9 12 10 0 0 +48 10 6 14 10 0 0 +49 8 10 13 9 0 0 +50 7 8 9 16 0 0 |
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| diff -r dbedfc5f5a3c -r 1421603cc95b test-data/output.NVC_plot.pdf |
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| diff -r dbedfc5f5a3c -r 1421603cc95b test-data/output.geneBodyCoverage2.curves.pdf |
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| Binary file test-data/output.geneBodyCoverage2.curves.pdf has changed |
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| diff -r dbedfc5f5a3c -r 1421603cc95b test-data/output.geneBodyCoverage2.txt --- a/test-data/output.geneBodyCoverage2.txt Sat Dec 18 19:41:19 2021 +0000 +++ b/test-data/output.geneBodyCoverage2.txt Sat Nov 26 15:19:14 2022 +0000 |
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| @@ -1,101 +1,101 @@ percentile count -0 0.0 -1 0.0 -2 0.0 -3 0.0 -4 0.0 -5 0.0 -6 0.0 -7 0.0 -8 0.0 -9 0.0 -10 0.0 -11 0.0 -12 0.0 -13 0.0 -14 0.0 -15 0.0 -16 0.0 -17 0.0 -18 0.0 -19 0.0 -20 0.0 -21 0.0 -22 0.0 -23 0.0 -24 0.0 -25 1.0 -26 0.0 -27 0.0 -28 1.0 -29 0.0 -30 0.0 -31 0.0 -32 0.0 -33 0.0 -34 0.0 -35 0.0 -36 0.0 -37 0.0 -38 1.0 -39 1.0 -40 1.0 -41 0.0 -42 0.0 -43 1.0 -44 1.0 -45 1.0 -46 0.0 -47 0.0 -48 0.0 -49 0.0 -50 0.0 -51 0.0 -52 0.0 -53 0.0 -54 0.0 -55 0.0 -56 0.0 -57 0.0 -58 0.0 -59 0.0 -60 0.0 -61 0.0 -62 0.0 -63 0.0 -64 0.0 -65 0.0 -66 0.0 -67 0.0 -68 0.0 -69 0.0 -70 0.0 -71 0.0 -72 0.0 -73 0.0 -74 0.0 -75 0.0 -76 0.0 -77 0.0 -78 0.0 -79 1.0 -80 1.0 -81 1.0 -82 0.0 -83 1.0 -84 1.0 -85 1.0 -86 0.0 -87 0.0 -88 0.0 -89 0.0 -90 0.0 -91 0.0 -92 0.0 -93 0.0 -94 0.0 -95 0.0 -96 0.0 -97 0.0 -98 0.0 -99 0.0 +0 0 +1 0 +2 0 +3 0 +4 0 +5 0 +6 0 +7 0 +8 0 +9 0 +10 0 +11 0 +12 0 +13 0 +14 0 +15 0 +16 0 +17 0 +18 0 +19 0 +20 0 +21 0 +22 0 +23 0 +24 0 +25 1 +26 0 +27 0 +28 1 +29 0 +30 0 +31 0 +32 0 +33 0 +34 0 +35 0 +36 0 +37 0 +38 1 +39 1 +40 1 +41 0 +42 0 +43 1 +44 1 +45 1 +46 0 +47 0 +48 0 +49 0 +50 0 +51 0 +52 0 +53 0 +54 0 +55 0 +56 0 +57 0 +58 0 +59 0 +60 0 +61 0 +62 0 +63 0 +64 0 +65 0 +66 0 +67 0 +68 0 +69 0 +70 0 +71 0 +72 0 +73 0 +74 0 +75 0 +76 0 +77 0 +78 0 +79 1 +80 1 +81 1 +82 0 +83 1 +84 1 +85 1 +86 0 +87 0 +88 0 +89 0 +90 0 +91 0 +92 0 +93 0 +94 0 +95 0 +96 0 +97 0 +98 0 +99 0 |
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| diff -r dbedfc5f5a3c -r 1421603cc95b test-data/output.geneBodyCoverage2_r --- a/test-data/output.geneBodyCoverage2_r Sat Dec 18 19:41:19 2021 +0000 +++ b/test-data/output.geneBodyCoverage2_r Sat Nov 26 15:19:14 2022 +0000 |
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| @@ -1,5 +1,5 @@ pdf('output.geneBodyCoverage.pdf') x=1:100 y=c(0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0,0.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,1.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0) -plot(x,y/7,xlab="percentile of gene body (5'->3')",ylab='average wigsum',type='s') +plot(x, y/7, xlab="percentile of gene body (5'->3')", ylab='average wigsum', type='s') dev.off() |
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| diff -r dbedfc5f5a3c -r 1421603cc95b test-data/output.inner_distance_plot.pdf |
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| Binary file test-data/output.inner_distance_plot.pdf has changed |
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| diff -r dbedfc5f5a3c -r 1421603cc95b test-data/output.inner_distance_plot_r --- a/test-data/output.inner_distance_plot_r Sat Dec 18 19:41:19 2021 +0000 +++ b/test-data/output.inner_distance_plot_r Sat Nov 26 15:19:14 2022 +0000 |
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| @@ -1,6 +1,6 @@ out_file = 'output' pdf('output.inner_distance_plot.pdf') -fragsize=rep(c(-248,-243,-238,-233,-228,-223,-218,-213,-208,-203,-198,-193,-188,-183,-178,-173,-168,-163,-158,-153,-148,-143,-138,-133,-128,-123,-118,-113,-108,-103,-98,-93,-88,-83,-78,-73,-68,-63,-58,-53,-48,-43,-38,-33,-28,-23,-18,-13,-8,-3,2,7,12,17,22,27,32,37,42,47,52,57,62,67,72,77,82,87,92,97,102,107,112,117,122,127,132,137,142,147,152,157,162,167,172,177,182,187,192,197,202,207,212,217,222,227,232,237,242,247),times=c(0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,1,0,1,0,0,2,0,0,2,0,0,0,1,0,1,1,0,0,0,1,0,0,0,0,0,0,0,0,1,0,0,1,0,1,0,0,0,0,0,0,0,1,0,1,1,0,1,0,1,0,0,0)) +fragsize=rep(c(-247.5,-242.5,-237.5,-232.5,-227.5,-222.5,-217.5,-212.5,-207.5,-202.5,-197.5,-192.5,-187.5,-182.5,-177.5,-172.5,-167.5,-162.5,-157.5,-152.5,-147.5,-142.5,-137.5,-132.5,-127.5,-122.5,-117.5,-112.5,-107.5,-102.5,-97.5,-92.5,-87.5,-82.5,-77.5,-72.5,-67.5,-62.5,-57.5,-52.5,-47.5,-42.5,-37.5,-32.5,-27.5,-22.5,-17.5,-12.5,-7.5,-2.5,2.5,7.5,12.5,17.5,22.5,27.5,32.5,37.5,42.5,47.5,52.5,57.5,62.5,67.5,72.5,77.5,82.5,87.5,92.5,97.5,102.5,107.5,112.5,117.5,122.5,127.5,132.5,137.5,142.5,147.5,152.5,157.5,162.5,167.5,172.5,177.5,182.5,187.5,192.5,197.5,202.5,207.5,212.5,217.5,222.5,227.5,232.5,237.5,242.5,247.5),times=c(0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,1,0,1,0,0,2,0,0,2,0,0,0,1,0,1,1,0,0,0,1,0,0,0,0,0,0,0,0,1,0,0,1,0,1,0,0,0,0,0,0,0,1,0,1,1,0,1,0,1,0,0,0)) frag_sd = sd(fragsize) frag_mean = mean(fragsize) frag_median = median(fragsize) |
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| diff -r dbedfc5f5a3c -r 1421603cc95b test-data/output.junction.xls --- a/test-data/output.junction.xls Sat Dec 18 19:41:19 2021 +0000 +++ b/test-data/output.junction.xls Sat Nov 26 15:19:14 2022 +0000 |
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| @@ -1,4 +1,4 @@ chrom intron_st(0-based) intron_end(1-based) read_count annotation -chr1 17055 17232 1 annotated -chr1 21768 22000 1 complete_novel -chr1 12697 13220 1 partial_novel +chr1 12697 13220 1 partial_novel +chr1 17055 17232 1 annotated +chr1 21768 22000 1 complete_novel |
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| diff -r dbedfc5f5a3c -r 1421603cc95b test-data/output.junction_plot_r --- a/test-data/output.junction_plot_r Sat Dec 18 19:41:19 2021 +0000 +++ b/test-data/output.junction_plot_r Sat Nov 26 15:19:14 2022 +0000 |
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| @@ -3,6 +3,6 @@ pie(events,col=c(2,3,4),init.angle=30,angle=c(60,120,150),density=c(70,70,70),main="splicing events",labels=c("partial_novel 25%","complete_novel 25%","known 25%")) dev.off() pdf("output.splice_junction.pdf") -junction=c(33.3333333333,33.3333333333,33.3333333333) +junction=c(33.333333333333336,33.333333333333336,33.333333333333336) pie(junction,col=c(2,3,4),init.angle=30,angle=c(60,120,150),density=c(70,70,70),main="splicing junctions",labels=c("partial_novel 33%","complete_novel 33%","known 33%")) dev.off() |
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| diff -r dbedfc5f5a3c -r 1421603cc95b test-data/output.splice_events.pdf |
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| diff -r dbedfc5f5a3c -r 1421603cc95b test-data/output.splice_junction.pdf |
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| diff -r dbedfc5f5a3c -r 1421603cc95b test-data/output.tin.xls --- a/test-data/output.tin.xls Sat Dec 18 19:41:19 2021 +0000 +++ b/test-data/output.tin.xls Sat Nov 26 15:19:14 2022 +0000 |
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| @@ -1,6 +1,6 @@ geneID chrom tx_start tx_end TIN NR_046018 chr1 11873 14409 0.0 -NR_024540 chr1 14361 29370 8.87096774194 +NR_024540 chr1 14361 29370 8.870967741935486 NR_106918 chr1 17368 17436 0.0 NR_107062 chr1 17368 17436 0.0 NR_026818 chr1 34610 36081 0.0 |
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| diff -r dbedfc5f5a3c -r 1421603cc95b test-data/summary.tin.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary.tin.txt Sat Nov 26 15:19:14 2022 +0000 |
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| @@ -0,0 +1,2 @@ +Bam_file TIN(mean) TIN(median) TIN(stdev) +pairend_strandspecific_51mer_hg19_chr1_1-100000_bam.bam 8.870967741935486 8.870967741935486 0.0 |
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| diff -r dbedfc5f5a3c -r 1421603cc95b test-data/testwig.Forward.wig --- a/test-data/testwig.Forward.wig Sat Dec 18 19:41:19 2021 +0000 +++ b/test-data/testwig.Forward.wig Sat Nov 26 15:19:14 2022 +0000 |
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| @@ -1,15 +1,3 @@ -variableStep chrom=chr13 -variableStep chrom=chr12 -variableStep chrom=chr11 -variableStep chrom=chr10 -variableStep chrom=chr17 -variableStep chrom=chr16 -variableStep chrom=chr15 -variableStep chrom=chr14 -variableStep chrom=chr19 -variableStep chrom=chr18 -variableStep chrom=chr8 -variableStep chrom=chr3 variableStep chrom=chr1 12674 1.00 12675 1.00 @@ -113,15 +101,27 @@ 13531 1.00 13532 1.00 13533 1.00 -variableStep chrom=chrY +variableStep chrom=chr2 +variableStep chrom=chr3 +variableStep chrom=chr4 +variableStep chrom=chr5 +variableStep chrom=chr6 +variableStep chrom=chr7 variableStep chrom=chrX +variableStep chrom=chr8 variableStep chrom=chr9 -variableStep chrom=chrM -variableStep chrom=chr22 +variableStep chrom=chr10 +variableStep chrom=chr11 +variableStep chrom=chr12 +variableStep chrom=chr13 +variableStep chrom=chr14 +variableStep chrom=chr15 +variableStep chrom=chr16 +variableStep chrom=chr17 +variableStep chrom=chr18 variableStep chrom=chr20 +variableStep chrom=chrY +variableStep chrom=chr19 +variableStep chrom=chr22 variableStep chrom=chr21 -variableStep chrom=chr7 -variableStep chrom=chr6 -variableStep chrom=chr5 -variableStep chrom=chr4 -variableStep chrom=chr2 +variableStep chrom=chrM |
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| diff -r dbedfc5f5a3c -r 1421603cc95b test-data/testwig.Reverse.wig --- a/test-data/testwig.Reverse.wig Sat Dec 18 19:41:19 2021 +0000 +++ b/test-data/testwig.Reverse.wig Sat Nov 26 15:19:14 2022 +0000 |
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| @@ -1,15 +1,3 @@ -variableStep chrom=chr13 -variableStep chrom=chr12 -variableStep chrom=chr11 -variableStep chrom=chr10 -variableStep chrom=chr17 -variableStep chrom=chr16 -variableStep chrom=chr15 -variableStep chrom=chr14 -variableStep chrom=chr19 -variableStep chrom=chr18 -variableStep chrom=chr8 -variableStep chrom=chr3 variableStep chrom=chr1 14596 -1.00 14597 -1.00 @@ -1672,15 +1660,27 @@ 94875 -1.00 94876 -1.00 94877 -1.00 -variableStep chrom=chrY +variableStep chrom=chr2 +variableStep chrom=chr3 +variableStep chrom=chr4 +variableStep chrom=chr5 +variableStep chrom=chr6 +variableStep chrom=chr7 variableStep chrom=chrX +variableStep chrom=chr8 variableStep chrom=chr9 -variableStep chrom=chrM -variableStep chrom=chr22 +variableStep chrom=chr10 +variableStep chrom=chr11 +variableStep chrom=chr12 +variableStep chrom=chr13 +variableStep chrom=chr14 +variableStep chrom=chr15 +variableStep chrom=chr16 +variableStep chrom=chr17 +variableStep chrom=chr18 variableStep chrom=chr20 +variableStep chrom=chrY +variableStep chrom=chr19 +variableStep chrom=chr22 variableStep chrom=chr21 -variableStep chrom=chr7 -variableStep chrom=chr6 -variableStep chrom=chr5 -variableStep chrom=chr4 -variableStep chrom=chr2 +variableStep chrom=chrM |
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| diff -r dbedfc5f5a3c -r 1421603cc95b test-data/testwig.wig --- a/test-data/testwig.wig Sat Dec 18 19:41:19 2021 +0000 +++ b/test-data/testwig.wig Sat Nov 26 15:19:14 2022 +0000 |
| b |
| @@ -1,15 +1,3 @@ -variableStep chrom=chr13 -variableStep chrom=chr12 -variableStep chrom=chr11 -variableStep chrom=chr10 -variableStep chrom=chr17 -variableStep chrom=chr16 -variableStep chrom=chr15 -variableStep chrom=chr14 -variableStep chrom=chr19 -variableStep chrom=chr18 -variableStep chrom=chr8 -variableStep chrom=chr3 variableStep chrom=chr1 12674 1.00 12675 1.00 @@ -1774,15 +1762,27 @@ 94875 1.00 94876 1.00 94877 1.00 -variableStep chrom=chrY +variableStep chrom=chr2 +variableStep chrom=chr3 +variableStep chrom=chr4 +variableStep chrom=chr5 +variableStep chrom=chr6 +variableStep chrom=chr7 variableStep chrom=chrX +variableStep chrom=chr8 variableStep chrom=chr9 -variableStep chrom=chrM -variableStep chrom=chr22 +variableStep chrom=chr10 +variableStep chrom=chr11 +variableStep chrom=chr12 +variableStep chrom=chr13 +variableStep chrom=chr14 +variableStep chrom=chr15 +variableStep chrom=chr16 +variableStep chrom=chr17 +variableStep chrom=chr18 variableStep chrom=chr20 +variableStep chrom=chrY +variableStep chrom=chr19 +variableStep chrom=chr22 variableStep chrom=chr21 -variableStep chrom=chr7 -variableStep chrom=chr6 -variableStep chrom=chr5 -variableStep chrom=chr4 -variableStep chrom=chr2 +variableStep chrom=chrM |
| b |
| diff -r dbedfc5f5a3c -r 1421603cc95b test-data/testwig_wigsum100.wig --- a/test-data/testwig_wigsum100.wig Sat Dec 18 19:41:19 2021 +0000 +++ b/test-data/testwig_wigsum100.wig Sat Nov 26 15:19:14 2022 +0000 |
| b |
| @@ -1,15 +1,3 @@ -variableStep chrom=chr13 -variableStep chrom=chr12 -variableStep chrom=chr11 -variableStep chrom=chr10 -variableStep chrom=chr17 -variableStep chrom=chr16 -variableStep chrom=chr15 -variableStep chrom=chr14 -variableStep chrom=chr19 -variableStep chrom=chr18 -variableStep chrom=chr8 -variableStep chrom=chr3 variableStep chrom=chr1 12674 0.05 12675 0.05 @@ -1774,15 +1762,27 @@ 94875 0.05 94876 0.05 94877 0.05 -variableStep chrom=chrY +variableStep chrom=chr2 +variableStep chrom=chr3 +variableStep chrom=chr4 +variableStep chrom=chr5 +variableStep chrom=chr6 +variableStep chrom=chr7 variableStep chrom=chrX +variableStep chrom=chr8 variableStep chrom=chr9 -variableStep chrom=chrM -variableStep chrom=chr22 +variableStep chrom=chr10 +variableStep chrom=chr11 +variableStep chrom=chr12 +variableStep chrom=chr13 +variableStep chrom=chr14 +variableStep chrom=chr15 +variableStep chrom=chr16 +variableStep chrom=chr17 +variableStep chrom=chr18 variableStep chrom=chr20 +variableStep chrom=chrY +variableStep chrom=chr19 +variableStep chrom=chr22 variableStep chrom=chr21 -variableStep chrom=chr7 -variableStep chrom=chr6 -variableStep chrom=chr5 -variableStep chrom=chr4 -variableStep chrom=chr2 +variableStep chrom=chrM |
| b |
| diff -r dbedfc5f5a3c -r 1421603cc95b tin.xml --- a/tin.xml Sat Dec 18 19:41:19 2021 +0000 +++ b/tin.xml Sat Nov 26 15:19:14 2022 +0000 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="rseqc_tin" name="Transcript Integrity Number" version="@TOOL_VERSION@.1"> +<tool id="rseqc_tin" name="Transcript Integrity Number" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@"> <description> evaluates RNA integrity at a transcript level </description> @@ -17,15 +17,26 @@ in the filename --> <command><![CDATA[ #import re - ln -sf '${input}' 'input.bam' && - ln -sf '${input.metadata.bam_index}' 'input.bam.bai' && - tin.py -i 'input.bam' --refgene='${refgene}' --minCov=${minCov} + #set $input_list = [] + #for $i, $input in enumerate($input): + #set $safename = re.sub('[^\w\-_]', '_', $input.element_identifier) + #if $safename in $input_list: + #set $safename = str($safename) + "." + str($i) + #end if + $input_list.append($safename) + ln -sf '${input}' '${safename}.bam' && + ln -sf '${input.metadata.bam_index}' '${safename}.bam.bai' && + echo '${safename}.bam' >> 'input_list.txt' && + #end for + tin.py -i 'input_list.txt' --refgene='${refgene}' --minCov=${minCov} --sample-size=${samplesize} ${subtractbackground} + && mv *summary.txt summary.tab + && mv *tin.xls tin.xls ]]> </command> <inputs> - <expand macro="bam_param" /> + <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)." /> @@ -41,22 +52,17 @@ </inputs> <outputs> - <data name="outputsummary" format="tabular" from_work_dir="input.summary.txt" label="TIN on ${on_string} (summary)" /> - <data name="outputxls" format="xls" from_work_dir="input.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="xls" from_work_dir="tin.xls" label="TIN on ${on_string} (tin)" /> </outputs> <!-- PDF Files contain R version, must avoid checking for diff --> <tests> - <test> + <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"/> - <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"/> + <output name="outputsummary" file="summary.tin.txt" ftype="tabular"/> + <output name="outputxls" file="output.tin.xls" ftype="xls"/> </test> </tests> |