Mercurial > repos > iuc > velocyto_cli
changeset 1:883c33ef3372 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit f523cd10a711b70ae4fef91a6e4dbc02781858b9
| author | iuc |
|---|---|
| date | Mon, 15 May 2023 10:03:38 +0000 |
| parents | 7d8cafa4d18c |
| children | 90e95e9ee190 |
| files | velocyto_cli.xml |
| diffstat | 1 files changed, 68 insertions(+), 17 deletions(-) [+] |
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--- a/velocyto_cli.xml Sat May 13 12:31:25 2023 +0000 +++ b/velocyto_cli.xml Mon May 15 10:03:38 2023 +0000 @@ -1,4 +1,4 @@ -<tool id="velocyto_cli" name="velocyto CLI" version="@VERSION@+galaxy0"> +<tool id="velocyto_cli" name="velocyto CLI" version="@VERSION@+galaxy1"> <description>pre-process data for the analysis of RNA velocity</description> <macros> <import>macros.xml</import> @@ -22,10 +22,15 @@ #import re #if str($main.do) == "run10x": + #if str($main.sample_definition.sample_definition_select) == "manual": + #set sample = str($main.sample_definition.sample) + #else: + #set sample = re.sub('[^\w\-\s]', '_', str($main.BAM.element_identifier)) + #end if ## We need to reproduce cell ranger structure: - mkdir -p '$main.sample/outs/filtered_gene_bc_matrices/whatever/' && - ln -s '${main.BAM}' '$main.sample/outs/possorted_genome_bam.bam' && - ln -s '${main.barcodes}' '$main.sample/outs/filtered_gene_bc_matrices/whatever/barcodes.tsv' && + mkdir -p '$sample/outs/filtered_gene_bc_matrices/whatever/' && + ln -s '${main.BAM}' '$sample/outs/possorted_genome_bam.bam' && + ln -s '${main.barcodes}' '$sample/outs/filtered_gene_bc_matrices/whatever/barcodes.tsv' && #else if str($main.do) in ['run', 'run-smartseq2']: #for $bam in $main.bamfiles: #set input_name = re.sub('[^\w\-\s]', '_', str($bam.element_identifier)) @@ -67,9 +72,9 @@ -t '$main.t' @SAMTOOLS_OPTS@ '$verbosity' - '$main.sample' + '$sample' '$main.gtffile' -&& mv '$main.sample/velocyto/'*.loom 'output.loom' +&& mv '$sample/velocyto/'*.loom 'output.loom' #else if str($main.do) == "run-smartseq2": run-smartseq2 @@ -119,14 +124,23 @@ <option value="dropest-bc-correct">Correct DropEst barcodes and produce valid barcodes file</option> </param> <when value="run10x" > - <param name="sample" type="text" value="sample" label="sample name" help="This name will appear as prefix of each cell barcode."> - <sanitizer invalid_char=""> - <valid initial="string.letters,string.digits"> - <add value="_" /> - </valid> - </sanitizer> - <validator type="regex">[0-9a-zA-Z_]+</validator> - </param> + <conditional name="sample_definition"> + <param name="sample_definition_select" type="select" label="How to set sample name" help="This name will appear as prefix of each cell barcode."> + <option value="manual">Manually</option> + <option value="identifier">Automatic (use identifier in history)</option> + </param> + <when value="manual"> + <param name="sample" type="text" value="sample" label="sample name" help=""> + <sanitizer invalid_char=""> + <valid initial="string.letters,string.digits"> + <add value="_" /> + </valid> + </sanitizer> + <validator type="regex">[0-9a-zA-Z_]+</validator> + </param> + </when> + <when value="identifier"/> + </conditional> <param name="BAM" type="data" format="bam" label="BAM file including CB tag" help="Can be Cell ranger output or STAR solo output" /> <param name="barcodes" type="data" format="tsv,tabular,txt" label="List of valid cell barcodes" help="Can be STAR solo barcodes output" /> <param name="gtffile" type="data" format="gtf" label="GTF file" /> @@ -192,7 +206,10 @@ <test expect_num_outputs="1"> <conditional name="main"> <param name="do" value="run10x"/> - <param name="sample" value="sample"/> + <conditional name="sample_definition"> + <param name="sample_definition_select" value="manual"/> + <param name="sample" value="sample"/> + </conditional> <param name="BAM" value="STARsolo_allSAMat.bam"/> <param name="barcodes" value="barcodes.tsv"/> <param name="gtffile" value="filtered3.Homo_sapiens.GRCh38.100.chr21.gtf"/> @@ -209,8 +226,11 @@ <metadata name="col_attrs_count" value="1" /> <metadata name="col_attrs_names" value="CellID" /> </output> + <assert_command> + <has_text text="sample"/> + </assert_command> <assert_stdout> - <has_text text="Counting for batch 1, containing 6 cells and 10 reads"/> + <has_text text="Counting for batch 1, containing 6 cells and 10 reads"/> </assert_stdout> </test> <!-- Test 2 run single bam as single cell --> @@ -262,7 +282,38 @@ <assert_stdout> <has_text text="Counting for batch 2, containing 1 cells and 716 reads"/> </assert_stdout> - </test> + </test> + <!-- Test 4 10x indentifyer --> + <test expect_num_outputs="1"> + <conditional name="main"> + <param name="do" value="run10x"/> + <conditional name="sample_definition"> + <param name="sample_definition_select" value="identifier"/> + </conditional> + <param name="BAM" value="STARsolo_allSAMat.bam"/> + <param name="barcodes" value="barcodes.tsv"/> + <param name="gtffile" value="filtered3.Homo_sapiens.GRCh38.100.chr21.gtf"/> + <param name="M" value="false"/> + <param name="t" value="uint16"/> + </conditional> + <output name="samples"> + <assert_contents> + <has_size value="25996" delta="3000"/> + </assert_contents> + <metadata name="row_attrs_count" value="6" /> + <metadata name="layers_count" value="3" /> + <metadata name="layers_names" value="ambiguous,spliced,unspliced" /> + <metadata name="col_attrs_count" value="1" /> + <metadata name="col_attrs_names" value="CellID" /> + </output> + <assert_command> + <has_text text="STARsolo_allSAMat"/> + <not_has_text text="sample"/> + </assert_command> + <assert_stdout> + <has_text text="Counting for batch 1, containing 6 cells and 10 reads"/> + </assert_stdout> + </test> </tests> <help><![CDATA[ Requirements on the input files