Mercurial > repos > iuc > bbtools_callvariants

comparison macros.xml @ 1:b955346ef41e draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
author iuc
date Thu, 11 Nov 2021 16:37:48 +0000
parents 18b91d72794b
children 85a34c9872b6
comparison
equal deleted inserted replaced
0:18b91d72794b 1:b955346ef41e
29 </action> 29 </action>
30 </when> 30 </when>
31 </conditional> 31 </conditional>
32 </actions> 32 </actions>
33 </macro> 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>
34 <macro name="reference_source_cond"> 53 <macro name="reference_source_cond">
35 <conditional name="ref_source_cond"> 54 <conditional name="ref_source_cond">
36 <param name="ref_source" type="select" label="Select reference genome source; a cached reference or one from the history"> 55 <param name="ref_source" type="select" label="Select reference genome source; a cached reference or one from the history">
37 <option value="cached" selected="True">Use a cached reference</option> 56 <option value="cached" selected="True">Use a cached reference</option>
38 <option value="history">Use a reference from the history</option> 57 <option value="history">Use a reference from the history</option>
44 <validator type="no_options" message="A built-in reference genome is not available"/> 63 <validator type="no_options" message="A built-in reference genome is not available"/>
45 </options> 64 </options>
46 </param> 65 </param>
47 </when> 66 </when>
48 <when value="history"> 67 <when value="history">
49 <param name="reference" type="data" format="fasta" label="Using reference genome"> 68 <param name="reference" type="data" format="fasta" label="Using reference genome"/>
50 <validator type="no_options" message="The current history does not include a fasta dataset"/> 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>
51 </param> 83 </param>
52 </when> 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>
53 </conditional> 86 </conditional>
54 </macro> 87 </macro>
55 <xml name="citations"> 88 <xml name="citations">
56 <citations> 89 <citations>
57 <citation type="doi"> 90 <citation type="doi">