Mercurial > repos > iuc > vsnp_determine_ref_from_data
diff vsnp_determine_ref_from_data.xml @ 1:b03e88e7bb1d draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2e312886647244b416c64eca91e1a61dd1be939b"
| author | iuc |
|---|---|
| date | Thu, 10 Dec 2020 15:25:22 +0000 |
| parents | 12f2b14549f6 |
| children | 6853676d2bae |
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--- a/vsnp_determine_ref_from_data.xml Wed Dec 02 09:11:24 2020 +0000 +++ b/vsnp_determine_ref_from_data.xml Thu Dec 10 15:25:22 2020 +0000 @@ -1,4 +1,4 @@ -<tool id="vsnp_determine_ref_from_data" name="vSNP: determine reference" version="1.0.0"> +<tool id="vsnp_determine_ref_from_data" name="vSNP: determine reference" version="@WRAPPER_VERSION@.1" profile="@PROFILE@"> <description>from input data</description> <macros> <import>macros.xml</import> @@ -25,10 +25,10 @@ #end if #else: #set read1 = $input_type_cond.reads_collection['forward'] - #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.element_identifier)) + #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.name)) ln -s '${read1}' '${read1_identifier}' && #set read2 = $input_type_cond.reads_collection['reverse'] - #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.element_identifier)) + #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.name)) ln -s '${read2}' '${read2_identifier}' && #end if @@ -67,8 +67,8 @@ </conditional> </inputs> <outputs> - <data name="output_dbkey" format="txt" label="${tool.name} (dbkey) on ${on_string}"/> - <data name="output_metrics" format="txt" label="${tool.name} (metrics) on ${on_string}"/> + <data name="output_dbkey" format="txt" label="${tool.name} on ${on_string} (dbkey)"/> + <data name="output_metrics" format="txt" label="${tool.name} on ${on_string} (metrics)"/> </outputs> <tests> <!-- 1 single read --> @@ -81,8 +81,8 @@ <!-- 1 set of paired reads --> <test expect_num_outputs="2"> <param name="input_type" value="pair"/> - <param name="read1" value="forward.fastq.gz" ftype="fastqsanger.gz"/> - <param name="read2" value="reverse.fastq.gz" ftype="fastqsanger.gz"/> + <param name="read1" value="CMC_20E1_R1.fastq.gz" ftype="fastqsanger.gz"/> + <param name="read2" value="CMC_20E1_R2.fastq.gz" ftype="fastqsanger.gz"/> <output name="output_dbkey" file="paired_dbkey.txt" ftype="txt"/> <output name="output_metrics" file="paired_metrics.txt" ftype="txt"/> </test> @@ -91,12 +91,12 @@ <param name="input_type" value="paired"/> <param name="reads_collection"> <collection type="paired"> - <element name="forward" value="forward.fastq.gz" ftype="fastqsanger.gz"/> - <element name="reverse" value="reverse.fastq.gz" ftype="fastqsanger.gz"/> + <element name="forward" value="CMC_20E1_R1.fastq.gz" ftype="fastqsanger.gz"/> + <element name="reverse" value="CMC_20E1_R2.fastq.gz" ftype="fastqsanger.gz"/> </collection> </param> <output name="output_dbkey" file="paired_dbkey.txt" ftype="txt"/> - <output name="output_metrics" file="paired_metrics.txt" ftype="txt"/> + <output name="output_metrics" file="paired_collection_metrics.txt" ftype="txt"/> </test> </tests> <help>