Mercurial > repos > iuc > bbtools_callvariants

annotate macros.xml @ 8:df9743790176 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 8f659e3524ff3fbf70ce9f4090e3fe8a49048b29
author iuc
date Wed, 24 Apr 2024 20:26:02 +0000
parents f36a69c3729a
children 66b138a2e74c
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
18b91d72794b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff changeset
1 <macros>
6
adec76ebc868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 8f77099ba7408b0bd15050c4845d900ec68fa6f3
iuc
parents: 4
diff changeset
2 <token name="@TOOL_VERSION@">39.06</token>
8
df9743790176 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 8f659e3524ff3fbf70ce9f4090e3fe8a49048b29
iuc
parents: 7
diff changeset
3 <token name="@VERSION_SUFFIX@">2</token>
4
8eace8923202 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents: 3
diff changeset
4 <token name="@PROFILE@">22.01</token>
8eace8923202 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents: 3
diff changeset
5 <xml name="edam_ontology">
8eace8923202 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents: 3
diff changeset
6 <edam_topics>
8eace8923202 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents: 3
diff changeset
7 <edam_topic>topic_0622</edam_topic> <!-- Genomics -->
8eace8923202 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents: 3
diff changeset
8 <edam_topic>topic_0091</edam_topic> <!-- Bioinformatics -->
8eace8923202 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents: 3
diff changeset
9 </edam_topics>
8eace8923202 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents: 3
diff changeset
10 <edam_operations>
8eace8923202 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents: 3
diff changeset
11 <edam_operation>operation_0496</edam_operation> <!-- Global alignment -->
8eace8923202 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents: 3
diff changeset
12 <edam_operation>operation_0491</edam_operation> <!-- Pairwise sequence alignment -->
8eace8923202 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents: 3
diff changeset
13 </edam_operations>
8eace8923202 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents: 3
diff changeset
14 </xml>
0
18b91d72794b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff changeset
15 <xml name="requirements">
18b91d72794b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff changeset
16 <requirements>
4
8eace8923202 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents: 3
diff changeset
17 <requirement type="package" version="@TOOL_VERSION@">bbmap</requirement>
6
adec76ebc868 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 8f77099ba7408b0bd15050c4845d900ec68fa6f3
iuc
parents: 4
diff changeset
18 <requirement type="package" version="1.19.2">samtools</requirement> <!-- automatic solving installs 1.6 in some cases, instead -->
0
18b91d72794b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff changeset
19 </requirements>
18b91d72794b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff changeset
20 </xml>
18b91d72794b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff changeset
21 <macro name="dbKeyActionsBBMap">
18b91d72794b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff changeset
22 <expand macro="dbKeyActions">
18b91d72794b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff changeset
23 <option type="from_data_table" name="fasta_indexes" column="1" offset="0">
18b91d72794b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff changeset
24 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
18b91d72794b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff changeset
25 <filter type="param_value" ref="ref_source_cond.reference" column="1"/>
18b91d72794b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff changeset
26 </option>
18b91d72794b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff changeset
27 </expand>
18b91d72794b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff changeset
28 </macro>
18b91d72794b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff changeset
29 <macro name="dbKeyActions">
18b91d72794b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff changeset
30 <actions>
18b91d72794b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff changeset
31 <conditional name="ref_source_cond.ref_source">
18b91d72794b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff changeset
32 <when value="cached">
18b91d72794b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff changeset
33 <action type="metadata" name="dbkey">
18b91d72794b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff changeset
34 <yield/>
18b91d72794b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff changeset
35 </action>
18b91d72794b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff changeset
36 </when>
18b91d72794b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff changeset
37 <when value="history">
18b91d72794b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff changeset
38 <action type="metadata" name="dbkey">
18b91d72794b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff changeset
39 <option type="from_param" name="ref_source_cond.reference" param_attribute="dbkey"/>
18b91d72794b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff changeset
40 </action>
18b91d72794b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff changeset
41 </when>
18b91d72794b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff changeset
42 </conditional>
18b91d72794b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff changeset
43 </actions>
18b91d72794b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff changeset
44 </macro>
1
b955346ef41e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents: 0
diff changeset
45 <macro name="input_type_cond">
b955346ef41e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents: 0
diff changeset
46 <conditional name="input_type_cond">
b955346ef41e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents: 0
diff changeset
47 <param name="input_type" type="select" label="Choose the category of the files to be analyzed">
b955346ef41e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents: 0
diff changeset
48 <option value="single" selected="true">Single dataset</option>
b955346ef41e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents: 0
diff changeset
49 <option value="pair">Dataset pair</option>
b955346ef41e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents: 0
diff changeset
50 <option value="paired">List of dataset pairs</option>
b955346ef41e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents: 0
diff changeset
51 </param>
b955346ef41e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents: 0
diff changeset
52 <when value="single">
2
85a34c9872b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 425671870866660485ef6a35c94d3736f5c1df97"
iuc
parents: 1
diff changeset
53 <param name="read1" type="data" format="fastqsanger.gz,fastqsanger" label="Fastq file"/>
1
b955346ef41e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents: 0
diff changeset
54 </when>
b955346ef41e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents: 0
diff changeset
55 <when value="pair">
2
85a34c9872b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 425671870866660485ef6a35c94d3736f5c1df97"
iuc
parents: 1
diff changeset
56 <param name="read1" type="data" format="fastqsanger.gz,fastqsanger" label="Forward reads fastq file"/>
85a34c9872b6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 425671870866660485ef6a35c94d3736f5c1df97"
iuc
parents: 1
diff changeset
57 <param name="read2" type="data" format="fastqsanger.gz,fastqsanger" label="Reverse reads fastq file"/>
1
b955346ef41e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents: 0
diff changeset
58 </when>
b955346ef41e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents: 0
diff changeset
59 <when value="paired">
b955346ef41e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents: 0
diff changeset
60 <param name="reads_collection" type="data_collection" format="fastqsanger,fastqsanger.gz" collection_type="paired" label="Collection of fastqsanger paired read files"/>
b955346ef41e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents: 0
diff changeset
61 </when>
b955346ef41e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents: 0
diff changeset
62 </conditional>
b955346ef41e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents: 0
diff changeset
63 </macro>
0
18b91d72794b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff changeset
64 <macro name="reference_source_cond">
18b91d72794b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff changeset
65 <conditional name="ref_source_cond">
18b91d72794b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff changeset
66 <param name="ref_source" type="select" label="Select reference genome source; a cached reference or one from the history">
18b91d72794b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff changeset
67 <option value="cached" selected="True">Use a cached reference</option>
18b91d72794b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff changeset
68 <option value="history">Use a reference from the history</option>
18b91d72794b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff changeset
69 </param>
18b91d72794b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff changeset
70 <when value="cached">
18b91d72794b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff changeset
71 <param name="reference" type="select" label="Using reference genome">
18b91d72794b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff changeset
72 <options from_data_table="fasta_indexes">
18b91d72794b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff changeset
73 <filter type="sort_by" column="2"/>
18b91d72794b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff changeset
74 <validator type="no_options" message="A built-in reference genome is not available"/>
18b91d72794b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff changeset
75 </options>
18b91d72794b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff changeset
76 </param>
18b91d72794b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff changeset
77 </when>
18b91d72794b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff changeset
78 <when value="history">
1
b955346ef41e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents: 0
diff changeset
79 <param name="reference" type="data" format="fasta" label="Using reference genome"/>
b955346ef41e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents: 0
diff changeset
80 </when>
b955346ef41e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents: 0
diff changeset
81 </conditional>
b955346ef41e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents: 0
diff changeset
82 </macro>
b955346ef41e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents: 0
diff changeset
83 <macro name="ktrim_cond">
b955346ef41e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents: 0
diff changeset
84 <conditional name="ktrim_cond">
b955346ef41e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents: 0
diff changeset
85 <param name="ktrim_select" type="select" label="Trim reads to remove bases matching reference kmers?">
b955346ef41e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents: 0
diff changeset
86 <option value="no" selected="true">No</option>
b955346ef41e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents: 0
diff changeset
87 <option value="yes">Yes</option>
b955346ef41e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents: 0
diff changeset
88 </param>
b955346ef41e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents: 0
diff changeset
89 <when value="no"/>
b955346ef41e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents: 0
diff changeset
90 <when value="yes">
b955346ef41e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents: 0
diff changeset
91 <param argument="ktrim" type="select" label="Select trimming position">
b955346ef41e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents: 0
diff changeset
92 <option value="r">Trim to the right</option>
b955346ef41e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents: 0
diff changeset
93 <option value="l">Trim to the left</option>
0
18b91d72794b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff changeset
94 </param>
1
b955346ef41e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents: 0
diff changeset
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."/>
b955346ef41e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents: 0
diff changeset
96 </when>
0
18b91d72794b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff changeset
97 </conditional>
18b91d72794b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff changeset
98 </macro>
18b91d72794b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff changeset
99 <xml name="citations">
18b91d72794b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff changeset
100 <citations>
18b91d72794b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff changeset
101 <citation type="doi">
18b91d72794b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff changeset
102 https://doi.org/10.1371/journal.pone.0185056
18b91d72794b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff changeset
103 </citation>
18b91d72794b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff changeset
104 </citations>
18b91d72794b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff changeset
105 </xml>
18b91d72794b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff changeset
106 </macros>
18b91d72794b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 56300a95740ee11e84a7d0bda07a71fbaf4952e4"
iuc
parents:
diff changeset
107