Mercurial > repos > iuc > bbtools_bbduk
comparison macros.xml @ 0:132af91f11b9 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
| author | iuc |
|---|---|
| date | Thu, 11 Nov 2021 16:36:50 +0000 |
| parents | |
| children | ff3b87a0d205 |
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| -1:000000000000 | 0:132af91f11b9 |
|---|---|
| 1 <macros> | |
| 2 <token name="@WRAPPER_VERSION@">1.0.0</token> | |
| 3 <token name="@VERSION_SUFFIX@">1.0.0</token> | |
| 4 <token name="@PROFILE@">20.09</token> | |
| 5 <xml name="requirements"> | |
| 6 <requirements> | |
| 7 <requirement type="package" version="38.92">bbmap</requirement> | |
| 8 </requirements> | |
| 9 </xml> | |
| 10 <macro name="dbKeyActionsBBMap"> | |
| 11 <expand macro="dbKeyActions"> | |
| 12 <option type="from_data_table" name="fasta_indexes" column="1" offset="0"> | |
| 13 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> | |
| 14 <filter type="param_value" ref="ref_source_cond.reference" column="1"/> | |
| 15 </option> | |
| 16 </expand> | |
| 17 </macro> | |
| 18 <macro name="dbKeyActions"> | |
| 19 <actions> | |
| 20 <conditional name="ref_source_cond.ref_source"> | |
| 21 <when value="cached"> | |
| 22 <action type="metadata" name="dbkey"> | |
| 23 <yield/> | |
| 24 </action> | |
| 25 </when> | |
| 26 <when value="history"> | |
| 27 <action type="metadata" name="dbkey"> | |
| 28 <option type="from_param" name="ref_source_cond.reference" param_attribute="dbkey"/> | |
| 29 </action> | |
| 30 </when> | |
| 31 </conditional> | |
| 32 </actions> | |
| 33 </macro> | |
| 34 <macro name="input_type_cond"> | |
| 35 <conditional name="input_type_cond"> | |
| 36 <param name="input_type" type="select" label="Choose the category of the files to be analyzed"> | |
| 37 <option value="single" selected="true">Single dataset</option> | |
| 38 <option value="pair">Dataset pair</option> | |
| 39 <option value="paired">List of dataset pairs</option> | |
| 40 </param> | |
| 41 <when value="single"> | |
| 42 <param name="read1" type="data" format="fastqsanger.gz,fastqsanger" label="Read1 fastq file"/> | |
| 43 </when> | |
| 44 <when value="pair"> | |
| 45 <param name="read1" type="data" format="fastqsanger.gz,fastqsanger" label="Read1 fastq file"/> | |
| 46 <param name="read2" type="data" format="fastqsanger.gz,fastqsanger" label="Read2 fastq file"/> | |
| 47 </when> | |
| 48 <when value="paired"> | |
| 49 <param name="reads_collection" type="data_collection" format="fastqsanger,fastqsanger.gz" collection_type="paired" label="Collection of fastqsanger paired read files"/> | |
| 50 </when> | |
| 51 </conditional> | |
| 52 </macro> | |
| 53 <macro name="reference_source_cond"> | |
| 54 <conditional name="ref_source_cond"> | |
| 55 <param name="ref_source" type="select" label="Select reference genome source; a cached reference or one from the history"> | |
| 56 <option value="cached" selected="True">Use a cached reference</option> | |
| 57 <option value="history">Use a reference from the history</option> | |
| 58 </param> | |
| 59 <when value="cached"> | |
| 60 <param name="reference" type="select" label="Using reference genome"> | |
| 61 <options from_data_table="fasta_indexes"> | |
| 62 <filter type="sort_by" column="2"/> | |
| 63 <validator type="no_options" message="A built-in reference genome is not available"/> | |
| 64 </options> | |
| 65 </param> | |
| 66 </when> | |
| 67 <when value="history"> | |
| 68 <param name="reference" type="data" format="fasta" label="Using reference genome"/> | |
| 69 </when> | |
| 70 </conditional> | |
| 71 </macro> | |
| 72 <macro name="ktrim_cond"> | |
| 73 <conditional name="ktrim_cond"> | |
| 74 <param name="ktrim_select" type="select" label="Trim reads to remove bases matching reference kmers?"> | |
| 75 <option value="no" selected="true">No</option> | |
| 76 <option value="yes">Yes</option> | |
| 77 </param> | |
| 78 <when value="no"/> | |
| 79 <when value="yes"> | |
| 80 <param argument="ktrim" type="select" label="Select trimming position"> | |
| 81 <option value="r">Trim to the right</option> | |
| 82 <option value="l">Trim to the left</option> | |
| 83 </param> | |
| 84 <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."/> | |
| 85 </when> | |
| 86 </conditional> | |
| 87 </macro> | |
| 88 <xml name="citations"> | |
| 89 <citations> | |
| 90 <citation type="doi"> | |
| 91 https://doi.org/10.1371/journal.pone.0185056 | |
| 92 </citation> | |
| 93 </citations> | |
| 94 </xml> | |
| 95 </macros> | |
| 96 |