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comparison macros.xml @ 0:fc029a9b4d07 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
author iuc
date Mon, 06 Feb 2023 18:06:47 +0000
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children 6d084528a6f1
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-1:000000000000 0:fc029a9b4d07
1 <macros>
2 <token name="@TOOL_VERSION@">39.01</token>
3 <token name="@VERSION_SUFFIX@">0</token>
4 <token name="@PROFILE@">22.01</token>
5 <xml name="edam_ontology">
6 <edam_topics>
7 <edam_topic>topic_0622</edam_topic> <!-- Genomics -->
8 <edam_topic>topic_0091</edam_topic> <!-- Bioinformatics -->
9 </edam_topics>
10 <edam_operations>
11 <edam_operation>operation_0496</edam_operation> <!-- Global alignment -->
12 <edam_operation>operation_0491</edam_operation> <!-- Pairwise sequence alignment -->
13 </edam_operations>
14 </xml>
15 <xml name="requirements">
16 <requirements>
17 <requirement type="package" version="@TOOL_VERSION@">bbmap</requirement>
18 <requirement type="package" version="1.16.1">samtools</requirement> <!-- automatic solving installs 1.6 in some cases, instead -->
19 </requirements>
20 </xml>
21 <macro name="dbKeyActionsBBMap">
22 <expand macro="dbKeyActions">
23 <option type="from_data_table" name="fasta_indexes" column="1" offset="0">
24 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
25 <filter type="param_value" ref="ref_source_cond.reference" column="1"/>
26 </option>
27 </expand>
28 </macro>
29 <macro name="dbKeyActions">
30 <actions>
31 <conditional name="ref_source_cond.ref_source">
32 <when value="cached">
33 <action type="metadata" name="dbkey">
34 <yield/>
35 </action>
36 </when>
37 <when value="history">
38 <action type="metadata" name="dbkey">
39 <option type="from_param" name="ref_source_cond.reference" param_attribute="dbkey"/>
40 </action>
41 </when>
42 </conditional>
43 </actions>
44 </macro>
45 <macro name="input_type_cond">
46 <conditional name="input_type_cond">
47 <param name="input_type" type="select" label="Choose the category of the files to be analyzed">
48 <option value="single" selected="true">Single dataset</option>
49 <option value="pair">Dataset pair</option>
50 <option value="paired">List of dataset pairs</option>
51 </param>
52 <when value="single">
53 <param name="read1" type="data" format="fastqsanger.gz,fastqsanger" label="Fastq file"/>
54 </when>
55 <when value="pair">
56 <param name="read1" type="data" format="fastqsanger.gz,fastqsanger" label="Forward reads fastq file"/>
57 <param name="read2" type="data" format="fastqsanger.gz,fastqsanger" label="Reverse reads fastq file"/>
58 </when>
59 <when value="paired">
60 <param name="reads_collection" type="data_collection" format="fastqsanger,fastqsanger.gz" collection_type="paired" label="Collection of fastqsanger paired read files"/>
61 </when>
62 </conditional>
63 </macro>
64 <macro name="reference_source_cond">
65 <conditional name="ref_source_cond">
66 <param name="ref_source" type="select" label="Select reference genome source; a cached reference or one from the history">
67 <option value="cached" selected="True">Use a cached reference</option>
68 <option value="history">Use a reference from the history</option>
69 </param>
70 <when value="cached">
71 <param name="reference" type="select" label="Using reference genome">
72 <options from_data_table="fasta_indexes">
73 <filter type="sort_by" column="2"/>
74 <validator type="no_options" message="A built-in reference genome is not available"/>
75 </options>
76 </param>
77 </when>
78 <when value="history">
79 <param name="reference" type="data" format="fasta" label="Using reference genome"/>
80 </when>
81 </conditional>
82 </macro>
83 <macro name="ktrim_cond">
84 <conditional name="ktrim_cond">
85 <param name="ktrim_select" type="select" label="Trim reads to remove bases matching reference kmers?">
86 <option value="no" selected="true">No</option>
87 <option value="yes">Yes</option>
88 </param>
89 <when value="no"/>
90 <when value="yes">
91 <param argument="ktrim" type="select" label="Select trimming position">
92 <option value="r">Trim to the right</option>
93 <option value="l">Trim to the left</option>
94 </param>
95 <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."/>
96 </when>
97 </conditional>
98 </macro>
99 <xml name="citations">
100 <citations>
101 <citation type="doi">
102 https://doi.org/10.1371/journal.pone.0185056
103 </citation>
104 </citations>
105 </xml>
106 </macros>
107