Mercurial > repos > lparsons > cutadapt

annotate macros.xml @ 39:fe74900d6dc7 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/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
author iuc
date Fri, 17 May 2024 13:32:03 +0000
parents b1c926deaa2d
children aa784cb3810d
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff changeset
1 <macros>
38
b1c926deaa2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c50d5611565c76ae9ed7fa9b2c6f65aba15e95d5
iuc
parents: 37
diff changeset
2 <token name="@TOOL_VERSION@">4.8</token>
39
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
3 <token name="@VERSION_SUFFIX@">1</token>
35
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 34
diff changeset
4 <token name="@FASTQ_TYPES@">fastq.bz2,fastq.gz,fastq,fasta.bz2,fasta.gz,fasta</token>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
5 <xml name="edam_ontology">
39
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
6 <edam_topics>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
7 <edam_topic>topic_0632</edam_topic>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
8 </edam_topics>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
9 <edam_operations>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
10 <edam_operation>operation_0231</edam_operation>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
11 </edam_operations>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
12 </xml>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
13 <xml name="requirements">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
14 <requirements>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
15 <requirement type="package" version="@TOOL_VERSION@">cutadapt</requirement>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
16 </requirements>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
17 </xml>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
18 <xml name="citations">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
19 <citations>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
20 <citation type="doi">10.14806/ej.17.1.200</citation>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
21 </citations>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
22 </xml>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
23 <xml name="xrefs">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
24 <xrefs>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
25 <xref type='bio.tools'>cutadapt</xref>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
26 </xrefs>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
27 </xml>
35
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 34
diff changeset
28 <!-- parametrized token - you need to set `$ADAPTER_ARGUMENT` -->
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 34
diff changeset
29 <token name="@adapter_cli@">
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 34
diff changeset
30 #if $a.adapter_source.adapter_source_list == 'builtin':
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 34
diff changeset
31 $ADAPTER_ARGUMENT '${a.adapter_source.adapter.fields.name}'='${a.adapter_source.adapter}${a.single_noindels}'
39
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
32 #elif $a.adapter_source.adapter_source_list == 'file':
35
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 34
diff changeset
33 $ADAPTER_ARGUMENT file:'${a.adapter_source.adapter_file}${a.single_noindels}'
39
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
34 #elif str($a.adapter_source.adapter_name) != "":
35
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 34
diff changeset
35 $ADAPTER_ARGUMENT '${a.adapter_source.adapter_name}'='${a.adapter_source.adapter}${a.single_noindels}'
39
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
36 #else:
35
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 34
diff changeset
37 $ADAPTER_ARGUMENT '${a.adapter_source.adapter}${a.single_noindels}'
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents:
diff changeset
38 #end if
39
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
39 </token>
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
40 <xml name="adapter_sanitizer">
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
41 <sanitizer>
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
42 <valid initial="string.digits">
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
43 <add value="A"/><!--standard nucleotides-->
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
44 <add value="T"/>
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
45 <add value="C"/>
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
46 <add value="G"/>
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
47 <add value="U"/><!--ambiguous nucleotides-->
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
48 <add value="R"/>
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
49 <add value="Y"/>
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
50 <add value="S"/>
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
51 <add value="W"/>
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
52 <add value="K"/>
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
53 <add value="M"/>
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
54 <add value="B"/>
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
55 <add value="D"/>
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
56 <add value="H"/>
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
57 <add value="V"/>
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
58 <add value="N"/>
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
59 <add value="X"/><!-- don't match any nucleotide-->
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
60 <add value="{"/><!--specify repeats .. needs digits which are added as default-->
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
61 <add value="}"/>
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
62 <add value="^"/><!--anchoring-->
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
63 <add value="$"/>
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
64 <add value="."/>
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
65 <add value="("/><!--specify what to keep-->
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
66 <add value=")"/>
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
67 </valid>
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
68 </sanitizer>
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
69 </xml>
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
70 <xml name="adapter_conditional" tokens="adapter_type,argument">
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
71 <conditional name="adapter_source">
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
72 <param name="adapter_source_list" type="select" label="Source" >
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
73 <option value="builtin" selected="true">Standard (select from the list below)</option>
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
74 <option value="user">Enter custom sequence</option>
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
75 <option value="file">File from history</option>
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
76 </param>
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
77 <when value="user">
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
78 <param name="adapter_name" type="text" value="" optional="true" label="Custom @ADAPTER_TYPE@ adapter name" help="Optional if 'Multiple output' is selected in the Outputs selector'" />
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
79 <param name="adapter" argument="@ARGUMENT@" type="text" value="AATTGGCC" label="Custom @ADAPTER_TYPE@ adapter sequence">
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
80 <expand macro="adapter_sanitizer"/>
35
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 34
diff changeset
81 </param>
39
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
82 </when>
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
83 <when value="builtin">
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
84 <param name="adapter" argument="@ARGUMENT@" type="select" label="@ADAPTER_TYPE@ adapter">
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
85 <options from_data_table="adapters">
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
86 <filter type="sort_by" column="1" />
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
87 </options>
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
88 <expand macro="adapter_sanitizer"/>
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
89 </param>
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
90 </when>
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
91 <when value="file">
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
92 <param name="adapter_file" argument="@ARGUMENT@" format="fasta" type="data" label="File containing @ADAPTER_TYPE@ adapters" help="Should be of datatype FASTA" />
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
93 </when>
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
94 </conditional>
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
95 <param name="single_noindels" type="boolean" truevalue=";noindels" falsevalue="" checked="false" label="Disallow indels for this adapter"/>
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
96 </xml>
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
97 <xml name="read1_adapters" >
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
98 <section name="r1" title="Read 1 Adapters" expanded="true">
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
99 <repeat name="adapters" title="3' (End) Adapters" help="Sequence of an adapter ligated to the 3' end (paired data: of the first read). The adapter and subsequent bases are trimmed. If a '$' character is appended ('anchoring'), the adapter is only found if it is a suffix of the read. To search for a linked adapter, separate the 2 sequences with 3 dots (ADAPTER1...ADAPTER2), see Help below.">
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
100 <expand macro="adapter_conditional" argument="-a" adapter_type="3'"/>
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
101 </repeat>
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
102 <repeat name="front_adapters" title="5' (Front) Adapters" help="Sequence of an adapter ligated to the 5' end (paired data: of the first read). The adapter and any preceding bases are trimmed. Partial matches at the 5' end are allowed. If a '^' character is prepended ('anchoring'), the adapter is only found if it is a prefix of the read. To search for a linked adapter, separate the 2 sequences with 3 dots (ADAPTER1...ADAPTER2), see Help below.">
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
103 <expand macro="adapter_conditional" argument="-g" adapter_type="5'"/>
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
104 </repeat>
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
105 <repeat name="anywhere_adapters" title="5' or 3' (Anywhere) Adapters" help="Sequence of an adapter that may be ligated to the 5' or 3' end (paired data: of the first read). Both types of matches as described under 3' und 5' Adapters are allowed. If the first base of the read is part of the match, the behavior is as with 5' Adapters, otherwise as with 3' Adapters. This option is mostly for rescuing failed library preparations - do not use if you know which end your adapter was ligated to!">
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
106 <expand macro="adapter_conditional" argument="-b" adapter_type="5' or 3'"/>
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
107 </repeat>
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
108 </section>
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
109 </xml>
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
110 <xml name="read2_adapters">
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
111 <section name="r2" title="Read 2 Adapters" expanded="true">
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
112 <repeat name="adapters2" title="3' (End) Adapters" help="Sequence of an adapter ligated to the 3' end of the second read in each pair. The adapter and subsequent bases are trimmed. If a '$' character is appended ('anchoring'), the adapter is only found if it is a suffix of the read. To search for a linked adapter, separate the 2 sequences with 3 dots (ADAPTER1...ADAPTER2), see Help below.">
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
113 <expand macro="adapter_conditional" argument="-A" adapter_type="3'"/>
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
114 </repeat>
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
115 <repeat name="front_adapters2" title="5' (Front) Adapters" help="Sequence of an adapter ligated to the 5' end of the second read in each pair. The adapter and any preceding bases are trimmed. Partial matches at the 5' end are allowed. If a '^' character is prepended ('anchoring'), the adapter is only found if it is a prefix of the read. To search for a linked adapter, separate the 2 sequences with 3 dots (ADAPTER1...ADAPTER2), see Help below.">
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
116 <expand macro="adapter_conditional" argument="-G" adapter_type="5'"/>
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
117 </repeat>
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
118 <repeat name="anywhere_adapters2" title="5' or 3' (Anywhere) Adapters" help="Sequence of an adapter that may be ligated to the 5' or 3' end of the second read in each pair. Both types of matches as described under under 3' und 5' Adapters are allowed. If the first base of the read is part of the match, the behavior is as with 5' Adapters, otherwise as with 3' Adapters. This option is mostly for rescuing failed library preparations - do not use if you know which end your adapter was ligated to!">
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
119 <expand macro="adapter_conditional" argument="-B" adapter_type="5' or 3'"/>
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
120 </repeat>
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
121 </section>
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
122 <param argument="--pair-adapters" type="boolean" truevalue="--pair-adapters" falsevalue="" label="Pairwise adapter search" help="The tool will normally look for R1 and R2 read adapters independently. By enabling this option you can have the lists of R1 and R2 read adapters handled pairwise instead. In this mode you need to provide equal numbers of R1 and R2 adapters of each type, or the tool will fail. For a more detailed explanation see the section Paired Adapters in the tool help below."/>
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
123 </xml>
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
124 <xml name="inherit_format_1">
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
125 <actions>
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
126 <conditional name="library.type">
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
127 <when value="single">
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
128 <action type="format">
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
129 <option type="from_param" name="library.input_1" param_attribute="ext" />
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
130 </action>
35
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 34
diff changeset
131 </when>
39
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
132 <when value="paired">
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
133 <action type="format">
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
134 <option type="from_param" name="library.input_1" param_attribute="ext" />
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
135 </action>
35
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 34
diff changeset
136 </when>
9845c649f41b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
iuc
parents: 34
diff changeset
137 </conditional>
39
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
138 </actions>
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
139 </xml>
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
140 <xml name="inherit_format_2">
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
141 <actions>
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
142 <conditional name="library.type">
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
143 <when value="paired">
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
144 <action type="format">
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
145 <option type="from_param" name="library.input_2" param_attribute="ext" />
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
146 </action>
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
147 </when>
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
148 </conditional>
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
149 </actions>
fe74900d6dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit a5b6cb44f81abe57a4269bded1fa4d41f462f9d5
iuc
parents: 38
diff changeset
150 </xml>
16
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 12
diff changeset
151 </macros>