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comparison macros.xml @ 9:83d0df824438 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit cd59ba2c349865259b92302a1d70e103b8a5e3cb
author iuc
date Tue, 27 Aug 2024 10:13:16 +0000
parents 3fa2af3231df
children 57136caabb32
comparison
equal deleted inserted replaced
8:33262f7b3e23 9:83d0df824438
1 <macros> 1 <macros>
2 <token name="@TOOL_VERSION@">39.01</token> 2 <token name="@TOOL_VERSION@">39.08</token>
3 <token name="@VERSION_SUFFIX@">0</token> 3 <token name="@VERSION_SUFFIX@">0</token>
4 <token name="@PROFILE@">22.01</token> 4 <token name="@PROFILE@">22.01</token>
5 <xml name="edam_ontology"> 5 <xml name="edam_ontology">
6 <edam_topics> 6 <edam_topics>
7 <edam_topic>topic_0622</edam_topic> <!-- Genomics --> 7 <edam_topic>topic_0622</edam_topic>
8 <edam_topic>topic_0091</edam_topic> <!-- Bioinformatics --> 8 <!-- Genomics -->
9 <edam_topic>topic_0091</edam_topic>
10 <!-- Bioinformatics -->
9 </edam_topics> 11 </edam_topics>
10 <edam_operations> 12 <edam_operations>
11 <edam_operation>operation_0496</edam_operation> <!-- Global alignment --> 13 <edam_operation>operation_0496</edam_operation>
12 <edam_operation>operation_0491</edam_operation> <!-- Pairwise sequence alignment --> 14 <!-- Global alignment -->
15 <edam_operation>operation_0491</edam_operation>
16 <!-- Pairwise sequence alignment -->
13 </edam_operations> 17 </edam_operations>
18 </xml>
19 <xml name="bio.tools">
20 <xrefs>
21 <xref type="bio.tools">bbtools</xref>
22 </xrefs>
14 </xml> 23 </xml>
15 <xml name="requirements"> 24 <xml name="requirements">
16 <requirements> 25 <requirements>
17 <requirement type="package" version="@TOOL_VERSION@">bbmap</requirement> 26 <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 --> 27 <requirement type="package" version="1.20">samtools</requirement>
28 <!-- automatic solving installs 1.6 in some cases, instead -->
19 </requirements> 29 </requirements>
20 </xml> 30 </xml>
21 <macro name="dbKeyActionsBBMap"> 31 <macro name="dbKeyActionsBBMap">
22 <expand macro="dbKeyActions"> 32 <expand macro="dbKeyActions">
23 <option type="from_data_table" name="fasta_indexes" column="1" offset="0"> 33 <option type="from_data_table" name="fasta_indexes" column="1" offset="0">
55 <when value="pair"> 65 <when value="pair">
56 <param name="read1" type="data" format="fastqsanger.gz,fastqsanger" label="Forward reads fastq file"/> 66 <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"/> 67 <param name="read2" type="data" format="fastqsanger.gz,fastqsanger" label="Reverse reads fastq file"/>
58 </when> 68 </when>
59 <when value="paired"> 69 <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"/> 70 <param name="reads_collection" type="data_collection" format="fastqsanger,fastqsanger.gz" label="Collection of fastqsanger paired read files" collection_type="paired"/>
61 </when> 71 </when>
62 </conditional> 72 </conditional>
63 </macro> 73 </macro>
64 <macro name="reference_source_cond"> 74 <macro name="reference_source_cond">
65 <conditional name="ref_source_cond"> 75 <conditional name="ref_source_cond">
80 </when> 90 </when>
81 </conditional> 91 </conditional>
82 </macro> 92 </macro>
83 <macro name="ktrim_cond"> 93 <macro name="ktrim_cond">
84 <conditional name="ktrim_cond"> 94 <conditional name="ktrim_cond">
85 <param name="ktrim_select" type="select" label="Trim reads to remove bases matching reference kmers?"> 95 <param name="ktrim_select" type="select" label="Trim reads to remove bases matching reference kmers?">
86 <option value="no" selected="true">No</option> 96 <option value="no" selected="true">No</option>
87 <option value="yes">Yes</option> 97 <option value="yes">Yes</option>
88 </param> 98 </param>
89 <when value="no"/> 99 <when value="no"/>
90 <when value="yes"> 100 <when value="yes">
91 <param argument="ktrim" type="select" label="Select trimming position"> 101 <param argument="ktrim" type="select" label="Select trimming position">
92 <option value="r">Trim to the right</option> 102 <option value="r">Trim to the right</option>
93 <option value="l">Trim to the left</option> 103 <option value="l">Trim to the left</option>
94 </param> 104 </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."/> 105 <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> 106 </when>
97 </conditional> 107 </conditional>
98 </macro> 108 </macro>
99 <xml name="citations"> 109 <xml name="citations">
100 <citations> 110 <citations>
101 <citation type="doi"> 111 <citation type="doi">
102 https://doi.org/10.1371/journal.pone.0185056 112 https://doi.org/10.1371/journal.pone.0185056
103 </citation> 113 </citation>
104 </citations> 114 </citations>
105 </xml> 115 </xml>
106 </macros> 116 </macros>
107