Mercurial > repos > iuc > bbtools_bbmerge
view macros.xml @ 0:fc029a9b4d07 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
author | iuc |
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date | Mon, 06 Feb 2023 18:06:47 +0000 |
parents | |
children | 6d084528a6f1 |
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<macros> <token name="@TOOL_VERSION@">39.01</token> <token name="@VERSION_SUFFIX@">0</token> <token name="@PROFILE@">22.01</token> <xml name="edam_ontology"> <edam_topics> <edam_topic>topic_0622</edam_topic> <!-- Genomics --> <edam_topic>topic_0091</edam_topic> <!-- Bioinformatics --> </edam_topics> <edam_operations> <edam_operation>operation_0496</edam_operation> <!-- Global alignment --> <edam_operation>operation_0491</edam_operation> <!-- Pairwise sequence alignment --> </edam_operations> </xml> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">bbmap</requirement> <requirement type="package" version="1.16.1">samtools</requirement> <!-- automatic solving installs 1.6 in some cases, instead --> </requirements> </xml> <macro name="dbKeyActionsBBMap"> <expand macro="dbKeyActions"> <option type="from_data_table" name="fasta_indexes" column="1" offset="0"> <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> <filter type="param_value" ref="ref_source_cond.reference" column="1"/> </option> </expand> </macro> <macro name="dbKeyActions"> <actions> <conditional name="ref_source_cond.ref_source"> <when value="cached"> <action type="metadata" name="dbkey"> <yield/> </action> </when> <when value="history"> <action type="metadata" name="dbkey"> <option type="from_param" name="ref_source_cond.reference" param_attribute="dbkey"/> </action> </when> </conditional> </actions> </macro> <macro name="input_type_cond"> <conditional name="input_type_cond"> <param name="input_type" type="select" label="Choose the category of the files to be analyzed"> <option value="single" selected="true">Single dataset</option> <option value="pair">Dataset pair</option> <option value="paired">List of dataset pairs</option> </param> <when value="single"> <param name="read1" type="data" format="fastqsanger.gz,fastqsanger" label="Fastq file"/> </when> <when value="pair"> <param name="read1" type="data" format="fastqsanger.gz,fastqsanger" label="Forward reads fastq file"/> <param name="read2" type="data" format="fastqsanger.gz,fastqsanger" label="Reverse reads fastq file"/> </when> <when value="paired"> <param name="reads_collection" type="data_collection" format="fastqsanger,fastqsanger.gz" collection_type="paired" label="Collection of fastqsanger paired read files"/> </when> </conditional> </macro> <macro name="reference_source_cond"> <conditional name="ref_source_cond"> <param name="ref_source" type="select" label="Select reference genome source; a cached reference or one from the history"> <option value="cached" selected="True">Use a cached reference</option> <option value="history">Use a reference from the history</option> </param> <when value="cached"> <param name="reference" type="select" label="Using reference genome"> <options from_data_table="fasta_indexes"> <filter type="sort_by" column="2"/> <validator type="no_options" message="A built-in reference genome is not available"/> </options> </param> </when> <when value="history"> <param name="reference" type="data" format="fasta" label="Using reference genome"/> </when> </conditional> </macro> <macro name="ktrim_cond"> <conditional name="ktrim_cond"> <param name="ktrim_select" type="select" label="Trim reads to remove bases matching reference kmers?"> <option value="no" selected="true">No</option> <option value="yes">Yes</option> </param> <when value="no"/> <when value="yes"> <param argument="ktrim" type="select" label="Select trimming position"> <option value="r">Trim to the right</option> <option value="l">Trim to the left</option> </param> <param argument="minlength" type="integer" value="10" label="Minimum read length" help="Trimmed reads shorter than this will be discarded, pairs will be discarded if both are shorter."/> </when> </conditional> </macro> <xml name="citations"> <citations> <citation type="doi"> https://doi.org/10.1371/journal.pone.0185056 </citation> </citations> </xml> </macros>