| Previous changeset 9:2568a3b975cb (2023-05-31) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit f173f58bc695c22364685c2ffbb9f3e95708f00f |
|
modified:
kallisto_quant.xml macros.xml |
| b |
| diff -r 2568a3b975cb -r 4f9c4e6566e5 kallisto_quant.xml --- a/kallisto_quant.xml Wed May 31 20:09:49 2023 +0000 +++ b/kallisto_quant.xml Mon Jun 05 22:06:44 2023 +0000 |
| b |
| b'@@ -32,12 +32,12 @@\n \'$single_reads\'\n #else:\n $single_paired.lib_type\n- #if str($single_paired.collection.collection_selector) == \'datasets\':\n- #set $forward_reads = $single_paired.collection.forward\n- #set $reverse_reads = $single_paired.collection.reverse\n+ #if str($single_paired.single_paired_selector) == \'paired_single\':\n+ #set $forward_reads = $single_paired.forward\n+ #set $reverse_reads = $single_paired.reverse\n #else:\n- #set $forward_reads = $single_paired.collection.reads.forward\n- #set $reverse_reads = $single_paired.collection.reads.reverse\n+ #set $forward_reads = $single_paired.reads.forward\n+ #set $reverse_reads = $single_paired.reads.reverse\n #end if\n #set $reads = "\'%s\' \'%s\'" % ($forward_reads, $reverse_reads)\n $reads\n@@ -59,32 +59,22 @@\n <conditional name="single_paired">\n <param name="single_paired_selector" type="select" label="Single-end or paired reads">\n <option value="single" selected="true">Single-end</option>\n- <option value="paired">Paired</option>\n+ <option value="paired_single">Paired.end (individual files)</option>\n+ <option value="paired_collection">Paired-end (collections)</option>\n </param>\n <when value="single">\n <param name="reads" type="data" format="fastq,fastq.gz" label="Reads in FASTQ format" />\n <param argument="--fragment-length" type="integer" value="200" label="Average fragment length" help="Illumina typically produces reads of 180-200bp" />\n <param argument="--sd" type="integer" value="20" label="Estimated standard deviation of fragment length" />\n </when>\n- <when value="paired">\n- <conditional name="collection">\n- <param name="collection_selector" type="select" label="Collection or individual datasets">\n- <option value="datasets" selected="true">Individual files</option>\n- <option value="collection">Pair or list of pairs</option>\n- </param>\n- <when value="datasets">\n- <param name="forward" type="data" format="fastq,fastq.gz" label="Forward reads" />\n- <param name="reverse" type="data" format="fastq,fastq.gz" label="Reverse reads" />\n- </when>\n- <when value="collection">\n- <param name="reads" type="data_collection" format="fastq,fastq.gz" collection_type="paired" label="Collection of reads" />\n- </when>\n- </conditional>\n- <param name="lib_type" type="select" label="Library strandness information">\n- <option value="">Unstranded</option>\n- <option value="--fr-stranded">Strand specific reads, first read forward</option>\n- <option value="--rf-stranded">Strand specific reads, first read reverse</option>\n- </param>\n+ <when value="paired_single">\n+ <param name="forward" type="data" format="fastq,fastq.gz" label="Forward reads" />\n+ <param name="reverse" type="data" format="fastq,fastq.gz" label="Reverse reads" />\n+ <expand macro="macro_lib_type"/>\n+ </when>\n+ <when value="paired_collection">\n+ <param name="reads" type="data_collection" format="fastq,fastq.gz" collection_type="paired" label="Collection of reads" />\n+ <expand macro="macro_lib_type"/>\n </when>\n </conditional>\n <param argument="--bias" type="boolean" truevalue="--bias" falsevalue="" label="Perform se'..b'me_source" value="history" />\n <param name="reference" ftype="fasta" value="mm10_chrM.fa" />\n- <param name="single_paired_selector" value="paired" />\n- <param name="collection_selector" value="datasets" />\n+ <param name="single_paired_selector" value="paired_single" />\n <param name="forward" ftype="fastq" value="mm10_chrM-1.f.fq" />\n <param name="reverse" ftype="fastq" value="mm10_chrM-1.r.fq" />\n <param name="lib_type" value="--fr-stranded"/>\n@@ -146,8 +134,7 @@\n <test>\n <param name="reference_transcriptome_source" value="history" />\n <param name="reference" ftype="fasta" value="mm10_chrM.fa" />\n- <param name="single_paired_selector" value="paired" />\n- <param name="collection_selector" value="collection" />\n+ <param name="single_paired_selector" value="paired_collection" />\n <param name="reads">\n <collection type="paired">\n <element name="forward" value="mm10_chrM-1.f.fq" />\n@@ -160,15 +147,13 @@\n <param name="reference_transcriptome_source" value="history" />\n <param name="reference" ftype="fasta" value="mm10_chrM.fa" />\n <param name="single_paired_selector" value="single" />\n- <param name="collection_selector" value="collection" />\n <param name="reads" ftype="fastq" value="mm10_chrM-1.f.fq" />\n <output name="abundance_tab" file="kallisto_quant_out3.tab" ftype="tabular" />\n </test>\n <test>\n <param name="reference_transcriptome_source" value="history" />\n <param name="reference" ftype="fasta" value="felCat8_chrM.fa" />\n- <param name="single_paired_selector" value="paired" />\n- <param name="collection_selector" value="datasets" />\n+ <param name="single_paired_selector" value="paired_single" />\n <param name="pseudobam" value="true" />\n <param name="forward" ftype="fastq" value="felCat8_chrM_F.fq" />\n <param name="reverse" ftype="fastq" value="felCat8_chrM_R.fq" />\n@@ -177,8 +162,7 @@\n </test>\n <test>\n <param name="reference_transcriptome_source" value="cached" />\n- <param name="single_paired_selector" value="paired" />\n- <param name="collection_selector" value="datasets" />\n+ <param name="single_paired_selector" value="paired_single" />\n <param name="pseudobam" value="true" />\n <param name="forward" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_F.fq.gz" />\n <param name="reverse" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_R.fq" />\n@@ -188,8 +172,7 @@\n <test>\n <param name="reference_transcriptome_source" value="history" />\n <param name="reference" ftype="fasta" value="hg38_transcripts.fa" />\n- <param name="single_paired_selector" value="paired" />\n- <param name="collection_selector" value="datasets" />\n+ <param name="single_paired_selector" value="paired_single" />\n <param name="fusion" value="true" />\n <param name="forward" ftype="fastq" dbkey="hg38" value="hg38_F.fq.gz" />\n <param name="reverse" ftype="fastq" dbkey="hg38" value="hg38_R.fq.gz" />\n@@ -198,8 +181,7 @@\n <test>\n <param name="reference_transcriptome_source" value="history" />\n <param name="reference" ftype="fasta" value="transcripts.fasta" />\n- <param name="single_paired_selector" value="paired" />\n- <param name="collection_selector" value="datasets" />\n+ <param name="single_paired_selector" value="paired_single" />\n <param name="forward" ftype="fastq" value="reads_forward.fastq.gz" />\n <param name="reverse" ftype="fastq" value="reads_reverse.fastq.gz" />\n <conditional name="genomebam_option">\n' |
| b |
| diff -r 2568a3b975cb -r 4f9c4e6566e5 macros.xml --- a/macros.xml Wed May 31 20:09:49 2023 +0000 +++ b/macros.xml Mon Jun 05 22:06:44 2023 +0000 |
| b |
| @@ -1,7 +1,7 @@ <?xml version="1.0"?> <macros> <token name="@TOOL_VERSION@">0.48.0</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">kallisto</requirement> @@ -32,4 +32,11 @@ </when> </conditional> </xml> + <xml name="macro_lib_type"> + <param name="lib_type" type="select" label="Library strandness information"> + <option value="">Unstranded</option> + <option value="--fr-stranded">Strand specific reads, first read forward</option> + <option value="--rf-stranded">Strand specific reads, first read reverse</option> + </param> + </xml> </macros> \ No newline at end of file |