| Previous changeset 2:1c75aa5de15e (2017-12-09) Next changeset 4:01247aaf0a10 (2021-04-06) |
|
Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit f84c314bc721b5b0c7be10eaf287b1830caca241" |
|
modified:
kallisto_pseudo.xml macros.xml test-data/kallisto_pseudo_out1.tab test-data/kallisto_pseudo_out6.tab |
| b |
| diff -r 1c75aa5de15e -r 5ae5c312d718 kallisto_pseudo.xml --- a/kallisto_pseudo.xml Sat Dec 09 05:34:01 2017 -0500 +++ b/kallisto_pseudo.xml Thu Sep 26 09:11:24 2019 -0400 |
| [ |
| @@ -15,13 +15,8 @@ #set index_path = $reference_transcriptome.index.fields.path #end if kallisto pseudo -i '$index_path' - #if $pseudobam: - $pseudobam -o . - #else: - --threads \${GALAXY_SLOTS:-1} - -o . - #end if - + --threads \${GALAXY_SLOTS:-1} + -o . #if str($single_paired.single_paired_selector) == 'single': --single --fragment-length $single_paired.fragment_length @@ -39,13 +34,10 @@ #end if #end if #end if - #if $pseudobam: - | samtools sort -O bam -@ \${GALAXY_SLOTS:-1} -o '$pseudobam_output' - - #end if && if [ -f run_info.json ] ; then cat run_info.json ; fi && mkdir outputs && if [ -f matrix.ec ] ; then mv matrix.ec outputs/Matrix.ec ; fi && - if [ -f matrix.tsv ] ; then mv matrix.tsv outputs/Matrix.tabular ; fi && + if [ -f matrix.tcc.mtx ] ; then mv matrix.tcc.mtx outputs/Matrix.tabular ; fi && if [ -f matrix.cells ] ; then mv matrix.cells outputs/Matrix.cells ; fi && if [ -f pseudoalignments.tsv ] ; then mv pseudoalignments.tsv outputs/Pseudoalignments.tabular ; fi && if [ -f pseudoalignments.ec ] ; then mv pseudoalignments.ec outputs/Pseudoalignments.ec ; fi @@ -106,15 +98,11 @@ </conditional> </when> </conditional> - <param argument="--pseudobam" type="boolean" truevalue="--pseudobam" falsevalue="" label="Output pseudoalignments in BAM format" /> </inputs> <outputs> <data format="tabular" name="sample"> <discover_datasets pattern="(?P<designation>.+)" directory="outputs" ext="tabular" visible="true" /> </data> - <data format="bam" name="pseudobam_output" label="${tool.name} on ${on_string}: Pseudoalignments (BAM)"> - <filter>pseudobam</filter> - </data> </outputs> <tests> <test> @@ -176,19 +164,6 @@ <param name="reference_transcriptome_source" value="cached" /> <param name="single_paired_selector" value="paired" /> <param name="collection_selector" value="datasets" /> - <param name="pseudobam" value="true" /> - <param name="forward" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_F.fq.gz" /> - <param name="reverse" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_R.fq.gz" /> - <output name="sample"> - <discovered_dataset designation="Pseudoalignments.tabular" file="kallisto_pseudo_out5.tab" ftype="tabular" /> - <discovered_dataset designation="Pseudoalignments.ec" file="kallisto_pseudo_out5.ec" ftype="tabular" /> - </output> - <output name="pseudobam_output" file="kallisto_pseudo_out5.bam" ftype="bam" /> - </test> - <test> - <param name="reference_transcriptome_source" value="cached" /> - <param name="single_paired_selector" value="paired" /> - <param name="collection_selector" value="datasets" /> <param name="umi" value="yes" /> <param name="forward" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM.umi" /> <param name="reverse" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_R.fq.gz" /> |
| b |
| diff -r 1c75aa5de15e -r 5ae5c312d718 macros.xml --- a/macros.xml Sat Dec 09 05:34:01 2017 -0500 +++ b/macros.xml Thu Sep 26 09:11:24 2019 -0400 |
| b |
| @@ -1,10 +1,10 @@ <?xml version="1.0"?> <macros> - <token name="@VERSION@">0.43.1</token> + <token name="@VERSION@">0.46.0</token> <xml name="requirements"> <requirements> <requirement type="package" version="@VERSION@">kallisto</requirement> - <requirement type="package" version="1.5">samtools</requirement> + <requirement type="package" version="1.9">samtools</requirement> </requirements> </xml> <xml name="citations"> |
| b |
| diff -r 1c75aa5de15e -r 5ae5c312d718 test-data/kallisto_pseudo_out1.tab --- a/test-data/kallisto_pseudo_out1.tab Sat Dec 09 05:34:01 2017 -0500 +++ b/test-data/kallisto_pseudo_out1.tab Thu Sep 26 09:11:24 2019 -0400 |
| b |
| @@ -1,2 +1,4 @@ -0 0 100 -0 1 100 +%%MatrixMarket matrix coordinate real general +2 1 2 +1 1 100 +2 1 100 |
| b |
| diff -r 1c75aa5de15e -r 5ae5c312d718 test-data/kallisto_pseudo_out6.tab --- a/test-data/kallisto_pseudo_out6.tab Sat Dec 09 05:34:01 2017 -0500 +++ b/test-data/kallisto_pseudo_out6.tab Thu Sep 26 09:11:24 2019 -0400 |
| b |
| @@ -1,2 +1,4 @@ -0 0 18 -0 1 18 +%%MatrixMarket matrix coordinate real general +2 1 2 +1 1 18 +2 1 18 |