| Previous changeset 0:581e52f03c5d (2015-05-20) Next changeset 2:2f804526f5fd (2017-11-09) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit bfa8bda732de882f6fa5f5375f8468ad229cceea |
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modified:
pear.xml tool_dependencies.xml |
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| diff -r 581e52f03c5d -r 240f611a46f3 pear.xml --- a/pear.xml Wed May 20 14:59:50 2015 -0400 +++ b/pear.xml Wed Nov 09 06:00:43 2016 -0500 |
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| @@ -1,6 +1,5 @@ -<tool id="iuc_pear" name="Pear" version="0.9.6.0"> +<tool id="iuc_pear" name="Pear" version="0.9.6.1"> <description>Paired-End read merger</description> - <!--<version_command>bismark version</version_command>--> <requirements> <requirement type="package" version="0.9.6">pear</requirement> </requirements> @@ -16,10 +15,20 @@ #if str( $library.type ) == "paired": -f "$library.forward" -r "$library.reverse" + #if $library.forward.is_of_type( 'fastqillumina' ): + --phred-base 64 + #else: + --phred-base 33 + #end if #else ## prepare collection - -f $library.input_collection.forward - -r $library.input_collection.reverse + -f "$library.input_collection.forward" + -r "$library.input_collection.reverse" + #if $library.input_collection.forward.is_of_type( 'fastqillumina' ): + --phred-base 64 + #else: + --phred-base 33 + #end if #end if --output pear @@ -47,15 +56,15 @@ <option value="paired_collection">Paired-end Dataset Collection</option> </param> <when value="paired"> - <param name="forward" type="data" format="fastqillumina, fastqsanger, fastq" + <param name="forward" type="data" format="fastqillumina,fastqsanger" label="Name of file that contains the forward paired-end reads" help="-f" /> - <param name="reverse" type="data" format="fastqillumina, fastqsanger, fastq" + <param name="reverse" type="data" format="fastqillumina,fastqsanger" label="Name of file that contains the reverse paired-end reads" help="-r" /> </when> <when value="paired_collection"> - <param name="input_collection" format="fastqillumina, fastqsanger, fastq" + <param name="input_collection" format="fastqillumina,fastqsanger" type="data_collection" collection_type="paired" - label="FASTQ Paired Dataset" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33. (-f and -r)" /> + label="FASTQ Paired Dataset" help="Nucleotide-space: Must have PHRED-scaled quality values. (-f and -r)" /> </when> </conditional> @@ -108,35 +117,34 @@ </param> </inputs> <outputs> - <data format="fastq" name="assembled_reads" from_work_dir="pear.assembled.fastq" label="${tool.name} on ${on_string}: Assembled reads"> + <data format="input" name="assembled_reads" from_work_dir="pear.assembled.fastq" label="${tool.name} on ${on_string}: Assembled reads"> <filter>'assembled' in outputs</filter> </data> - <data format="fastq" name="unassembled_forward_reads" from_work_dir="pear.unassembled.forward.fastq" label="${tool.name} on ${on_string}: Unassembled forward reads"> + <data format="input" name="unassembled_forward_reads" from_work_dir="pear.unassembled.forward.fastq" label="${tool.name} on ${on_string}: Unassembled forward reads"> <filter>'forward' in outputs</filter> </data> - <data format="fastq" name="unassembled_reverse_reads" from_work_dir="pear.unassembled.reverse.fastq" label="${tool.name} on ${on_string}: Unassembled reverse reads"> + <data format="input" name="unassembled_reverse_reads" from_work_dir="pear.unassembled.reverse.fastq" label="${tool.name} on ${on_string}: Unassembled reverse reads"> <filter>'reverse' in outputs</filter> </data> - <data format="fastq" name="discarded_reads" from_work_dir="pear.discarded.fastq" label="${tool.name} on ${on_string}: Discarded reads"> + <data format="input" name="discarded_reads" from_work_dir="pear.discarded.fastq" label="${tool.name} on ${on_string}: Discarded reads"> <filter>'discarded' in outputs</filter> </data> </outputs> <tests> <test> - <param name="forward" value="forward.fastq" ftype="fastq" /> - <param name="reverse" value="reverse.fastq" ftype="fastq" /> + <param name="forward" value="forward.fastq" ftype="fastqsanger" /> + <param name="reverse" value="reverse.fastq" ftype="fastqsanger" /> <param name="min_overlap" value="10" /> <param name="min_assembly_length" value="50" /> <param name="cap" value="0" /> <param name="outputs" value="assembled,forward" /> - <output name="assembled_reads" file="pear_assembled_results1.fastq" ftype="fastq"/> - <output name="unassembled_forward_reads" file="pear_unassembled_forward_results1.fastq" ftype="fastq"/> + <output name="assembled_reads" file="pear_assembled_results1.fastq" ftype="fastqsanger"/> + <output name="unassembled_forward_reads" file="pear_unassembled_forward_results1.fastq" ftype="fastqsanger"/> </test> </tests> <help> <![CDATA[ - **What it does** PEAR_ is an ultrafast, memory-efficient and highly accurate pair-end read merger. |
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| diff -r 581e52f03c5d -r 240f611a46f3 tool_dependencies.xml --- a/tool_dependencies.xml Wed May 20 14:59:50 2015 -0400 +++ b/tool_dependencies.xml Wed Nov 09 06:00:43 2016 -0500 |
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| @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> - <package name="pear" version="0.9.6"> - <repository changeset_revision="833c4be8f4d4" name="package_pear_0_9_6" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + <package name="pear" version="0.9.6"> + <repository changeset_revision="833c4be8f4d4" name="package_pear_0_9_6" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency> |