comparison macros.xml @ 0:204a131e47db draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
author iuc
date Thu, 11 Nov 2021 16:38:32 +0000
parents
children 60dd895841cd
comparison
equal deleted inserted replaced
-1:000000000000 0:204a131e47db
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