annotate data_manager/macros.xml @ 11:d63c1442407f draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 096286097ed5cdf189a1b68c3fc34d10f4142e54
author iuc
date Sun, 16 Apr 2023 08:31:33 +0000
parents a225487bf618
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
cdc4d8a998e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
diff changeset
1 <macros>
10
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
2 <!-- REMEMBER to bump the version of @IDX_VERSION_SUFFIX@
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
3 whenever you make changes to the @TOOL_VERSION@ token!
6
64deddb6a8ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 57f71aa633a43ab02bbf05acd0c6d7f406e01f1e"
iuc
parents: 5
diff changeset
4 The data manager uses a symlink to this macro file to keep the STAR and
10
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
5 the index versions in sync, but you should manually update @IDX_VERSION_SUFFIX@ -->
5
f5eb9afa8f8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 9b68f6ae375aed38493f8399b8572347c750336d
iuc
parents: 4
diff changeset
6 <!-- STAR version to be used -->
10
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
7 <token name="@TOOL_VERSION@">2.7.10b</token>
11
d63c1442407f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 096286097ed5cdf189a1b68c3fc34d10f4142e54
iuc
parents: 10
diff changeset
8 <token name="@VERSION_SUFFIX@">3</token>
10
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
9 <token name="@PROFILE@">21.01</token>
5
f5eb9afa8f8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 9b68f6ae375aed38493f8399b8572347c750336d
iuc
parents: 4
diff changeset
10 <!-- STAR index version compatible with this version of STAR
f5eb9afa8f8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 9b68f6ae375aed38493f8399b8572347c750336d
iuc
parents: 4
diff changeset
11 This is the STAR version that introduced the index structure expected
f5eb9afa8f8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 9b68f6ae375aed38493f8399b8572347c750336d
iuc
parents: 4
diff changeset
12 by the current version.
f5eb9afa8f8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 9b68f6ae375aed38493f8399b8572347c750336d
iuc
parents: 4
diff changeset
13 It can be found for any specific version of STAR with:
f5eb9afa8f8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 9b68f6ae375aed38493f8399b8572347c750336d
iuc
parents: 4
diff changeset
14 STAR -h | grep versionGenome
f5eb9afa8f8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 9b68f6ae375aed38493f8399b8572347c750336d
iuc
parents: 4
diff changeset
15 or by looking for the versionGenome parameter in source/parametersDefault
f5eb9afa8f8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 9b68f6ae375aed38493f8399b8572347c750336d
iuc
parents: 4
diff changeset
16 of STAR's source code -->
7
6c6c6df09e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 6
diff changeset
17 <token name="@IDX_VERSION@">2.7.4a</token>
10
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
18 <token name="@IDX_VERSION_SUFFIX@">1</token>
7
6c6c6df09e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 6
diff changeset
19 <token name="@IDX_DATA_TABLE@">rnastar_index2x_versioned</token>
5
f5eb9afa8f8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 9b68f6ae375aed38493f8399b8572347c750336d
iuc
parents: 4
diff changeset
20
1
cdc4d8a998e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
diff changeset
21 <xml name="requirements">
cdc4d8a998e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
diff changeset
22 <requirements>
10
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
23 <requirement type="package" version="@TOOL_VERSION@">star</requirement>
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
24 <requirement type="package" version="1.16.1">samtools</requirement>
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
25 <requirement type="package" version="1.12">gzip</requirement>
6
64deddb6a8ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 57f71aa633a43ab02bbf05acd0c6d7f406e01f1e"
iuc
parents: 5
diff changeset
26 <yield />
1
cdc4d8a998e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
diff changeset
27 </requirements>
cdc4d8a998e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
diff changeset
28 </xml>
5
f5eb9afa8f8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 9b68f6ae375aed38493f8399b8572347c750336d
iuc
parents: 4
diff changeset
29
9
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
30 <xml name="edam">
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
31 <edam_topics>
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
32 <edam_topic>topic_3170</edam_topic>
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
33 <edam_topic>topic_3308</edam_topic>
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
34 </edam_topics>
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
35 <edam_operations>
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
36 <edam_operation>operation_0292</edam_operation>
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
37 </edam_operations>
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
38 </xml>
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
39
6
64deddb6a8ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 57f71aa633a43ab02bbf05acd0c6d7f406e01f1e"
iuc
parents: 5
diff changeset
40 <xml name="index_selection" token_with_gene_model="0">
10
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
41 <param argument="--genomeDir" type="select"
5
f5eb9afa8f8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 9b68f6ae375aed38493f8399b8572347c750336d
iuc
parents: 4
diff changeset
42 label="Select reference genome"
f5eb9afa8f8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 9b68f6ae375aed38493f8399b8572347c750336d
iuc
parents: 4
diff changeset
43 help="If your genome of interest is not listed, contact the Galaxy team">
7
6c6c6df09e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 6
diff changeset
44 <options from_data_table="@IDX_DATA_TABLE@">
5
f5eb9afa8f8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 9b68f6ae375aed38493f8399b8572347c750336d
iuc
parents: 4
diff changeset
45 <filter type="static_value" column="4" value="@WITH_GENE_MODEL@" />
f5eb9afa8f8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 9b68f6ae375aed38493f8399b8572347c750336d
iuc
parents: 4
diff changeset
46 <filter type="static_value" column="5" value="@IDX_VERSION@" />
f5eb9afa8f8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 9b68f6ae375aed38493f8399b8572347c750336d
iuc
parents: 4
diff changeset
47 <filter type="sort_by" column="2" />
f5eb9afa8f8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 9b68f6ae375aed38493f8399b8572347c750336d
iuc
parents: 4
diff changeset
48 <validator type="no_options" message="No indexes are available for the selected input dataset" />
f5eb9afa8f8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 9b68f6ae375aed38493f8399b8572347c750336d
iuc
parents: 4
diff changeset
49 </options>
f5eb9afa8f8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 9b68f6ae375aed38493f8399b8572347c750336d
iuc
parents: 4
diff changeset
50 </param>
f5eb9afa8f8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 9b68f6ae375aed38493f8399b8572347c750336d
iuc
parents: 4
diff changeset
51 </xml>
f5eb9afa8f8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 9b68f6ae375aed38493f8399b8572347c750336d
iuc
parents: 4
diff changeset
52
1
cdc4d8a998e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
diff changeset
53 <token name="@FASTQ_GZ_OPTION@">
cdc4d8a998e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
diff changeset
54 --readFilesCommand zcat
cdc4d8a998e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
diff changeset
55 </token>
cdc4d8a998e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
diff changeset
56 <xml name="citations">
cdc4d8a998e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
diff changeset
57 <citations>
cdc4d8a998e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
diff changeset
58 <citation type="doi">10.1093/bioinformatics/bts635</citation>
cdc4d8a998e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
diff changeset
59 </citations>
cdc4d8a998e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
diff changeset
60 </xml>
10
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
61 <xml name="SJDBOPTIONS">
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
62 <param argument="--sjdbGTFfile" type="data" format="gff3,gtf" label="Gene model (gff3,gtf) file for splice junctions" optional="false" help="Exon junction information for mapping splices"/>
1
cdc4d8a998e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
diff changeset
63 <param argument="--sjdbOverhang" type="integer" min="1" value="100" label="Length of the genomic sequence around annotated junctions" help="Used in constructing the splice junctions database. Ideal value is ReadLength-1"/>
cdc4d8a998e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
diff changeset
64 </xml>
4
6ef6520f14fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 39b9b154845ecf517f7d9e9d76c386b473c3ebd2
iuc
parents: 1
diff changeset
65 <xml name="dbKeyActions">
6ef6520f14fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 39b9b154845ecf517f7d9e9d76c386b473c3ebd2
iuc
parents: 1
diff changeset
66 <actions>
11
d63c1442407f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 096286097ed5cdf189a1b68c3fc34d10f4142e54
iuc
parents: 10
diff changeset
67 <expand macro="dbKeyAction"/>
4
6ef6520f14fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 39b9b154845ecf517f7d9e9d76c386b473c3ebd2
iuc
parents: 1
diff changeset
68 </actions>
6ef6520f14fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 39b9b154845ecf517f7d9e9d76c386b473c3ebd2
iuc
parents: 1
diff changeset
69 </xml>
11
d63c1442407f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 096286097ed5cdf189a1b68c3fc34d10f4142e54
iuc
parents: 10
diff changeset
70 <xml name="dbKeyAction">
d63c1442407f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 096286097ed5cdf189a1b68c3fc34d10f4142e54
iuc
parents: 10
diff changeset
71 <conditional name="refGenomeSource.geneSource">
d63c1442407f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 096286097ed5cdf189a1b68c3fc34d10f4142e54
iuc
parents: 10
diff changeset
72 <when value="indexed">
d63c1442407f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 096286097ed5cdf189a1b68c3fc34d10f4142e54
iuc
parents: 10
diff changeset
73 <action type="metadata" name="dbkey">
d63c1442407f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 096286097ed5cdf189a1b68c3fc34d10f4142e54
iuc
parents: 10
diff changeset
74 <option type="from_data_table" name="@IDX_DATA_TABLE@" column="1" offset="0">
d63c1442407f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 096286097ed5cdf189a1b68c3fc34d10f4142e54
iuc
parents: 10
diff changeset
75 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
d63c1442407f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 096286097ed5cdf189a1b68c3fc34d10f4142e54
iuc
parents: 10
diff changeset
76 <filter type="param_value" ref="refGenomeSource.GTFconditional.genomeDir" column="0"/>
d63c1442407f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 096286097ed5cdf189a1b68c3fc34d10f4142e54
iuc
parents: 10
diff changeset
77 </option>
d63c1442407f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 096286097ed5cdf189a1b68c3fc34d10f4142e54
iuc
parents: 10
diff changeset
78 </action>
d63c1442407f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 096286097ed5cdf189a1b68c3fc34d10f4142e54
iuc
parents: 10
diff changeset
79 </when>
d63c1442407f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 096286097ed5cdf189a1b68c3fc34d10f4142e54
iuc
parents: 10
diff changeset
80 <when value="history">
d63c1442407f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 096286097ed5cdf189a1b68c3fc34d10f4142e54
iuc
parents: 10
diff changeset
81 <action type="metadata" name="dbkey">
d63c1442407f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 096286097ed5cdf189a1b68c3fc34d10f4142e54
iuc
parents: 10
diff changeset
82 <option type="from_param" name="refGenomeSource.genomeFastaFiles" param_attribute="dbkey" />
d63c1442407f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 096286097ed5cdf189a1b68c3fc34d10f4142e54
iuc
parents: 10
diff changeset
83 </action>
d63c1442407f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 096286097ed5cdf189a1b68c3fc34d10f4142e54
iuc
parents: 10
diff changeset
84 </when>
d63c1442407f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 096286097ed5cdf189a1b68c3fc34d10f4142e54
iuc
parents: 10
diff changeset
85 </conditional>
d63c1442407f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 096286097ed5cdf189a1b68c3fc34d10f4142e54
iuc
parents: 10
diff changeset
86 </xml>
5
f5eb9afa8f8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 9b68f6ae375aed38493f8399b8572347c750336d
iuc
parents: 4
diff changeset
87 <token name="@TEMPINDEX@"><![CDATA[
f5eb9afa8f8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 9b68f6ae375aed38493f8399b8572347c750336d
iuc
parents: 4
diff changeset
88 ## Create temporary index for custom reference
f5eb9afa8f8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 9b68f6ae375aed38493f8399b8572347c750336d
iuc
parents: 4
diff changeset
89 #if str($refGenomeSource.geneSource) == 'history':
10
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
90 #if $refGenomeSource.genomeFastaFiles.ext == "fasta"
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
91 ln -s '$refGenomeSource.genomeFastaFiles' refgenome.fa &&
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
92 #else
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
93 gunzip -c '$refGenomeSource.genomeFastaFiles' > refgenome.fa &&
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
94 #end if
5
f5eb9afa8f8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 9b68f6ae375aed38493f8399b8572347c750336d
iuc
parents: 4
diff changeset
95 mkdir -p tempstargenomedir &&
f5eb9afa8f8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 9b68f6ae375aed38493f8399b8572347c750336d
iuc
parents: 4
diff changeset
96 STAR
f5eb9afa8f8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 9b68f6ae375aed38493f8399b8572347c750336d
iuc
parents: 4
diff changeset
97 --runMode genomeGenerate
f5eb9afa8f8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 9b68f6ae375aed38493f8399b8572347c750336d
iuc
parents: 4
diff changeset
98 --genomeDir 'tempstargenomedir'
10
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
99 --genomeFastaFiles refgenome.fa
5
f5eb9afa8f8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 9b68f6ae375aed38493f8399b8572347c750336d
iuc
parents: 4
diff changeset
100 ## Handle difference between indices with/without annotations
7
6c6c6df09e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 6
diff changeset
101 #if 'GTFconditional' in $refGenomeSource:
6c6c6df09e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 6
diff changeset
102 ## GTFconditional exists only in STAR, but not STARsolo
6c6c6df09e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 6
diff changeset
103 #if str($refGenomeSource.GTFconditional.GTFselect) == 'with-gtf':
6c6c6df09e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 6
diff changeset
104 --sjdbOverhang '${refGenomeSource.GTFconditional.sjdbOverhang}'
6c6c6df09e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 6
diff changeset
105 --sjdbGTFfile '${refGenomeSource.GTFconditional.sjdbGTFfile}'
6c6c6df09e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 6
diff changeset
106 #if str($refGenomeSource.GTFconditional.sjdbGTFfile.ext) == 'gff3':
6c6c6df09e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 6
diff changeset
107 --sjdbGTFtagExonParentTranscript Parent
6c6c6df09e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 6
diff changeset
108 #end if
6c6c6df09e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 6
diff changeset
109 #end if
6c6c6df09e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 6
diff changeset
110 #else:
6c6c6df09e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 6
diff changeset
111 ## ref genome selection is less complex for STARsolo cause
6c6c6df09e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 6
diff changeset
112 ## with-gtf is mandatory there
6c6c6df09e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 6
diff changeset
113 --sjdbOverhang '${refGenomeSource.sjdbOverhang}'
6c6c6df09e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 6
diff changeset
114 --sjdbGTFfile '${refGenomeSource.sjdbGTFfile}'
6c6c6df09e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 6
diff changeset
115 #if str($refGenomeSource.sjdbGTFfile.ext) == 'gff3':
5
f5eb9afa8f8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 9b68f6ae375aed38493f8399b8572347c750336d
iuc
parents: 4
diff changeset
116 --sjdbGTFtagExonParentTranscript Parent
f5eb9afa8f8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 9b68f6ae375aed38493f8399b8572347c750336d
iuc
parents: 4
diff changeset
117 #end if
f5eb9afa8f8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 9b68f6ae375aed38493f8399b8572347c750336d
iuc
parents: 4
diff changeset
118 #end if
f5eb9afa8f8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 9b68f6ae375aed38493f8399b8572347c750336d
iuc
parents: 4
diff changeset
119 #if str($refGenomeSource.genomeSAindexNbases):
f5eb9afa8f8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 9b68f6ae375aed38493f8399b8572347c750336d
iuc
parents: 4
diff changeset
120 --genomeSAindexNbases ${refGenomeSource.genomeSAindexNbases}
f5eb9afa8f8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 9b68f6ae375aed38493f8399b8572347c750336d
iuc
parents: 4
diff changeset
121 #end if
f5eb9afa8f8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 9b68f6ae375aed38493f8399b8572347c750336d
iuc
parents: 4
diff changeset
122 --runThreadN \${GALAXY_SLOTS:-4}
10
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
123 ## in bytes
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
124 --limitGenomeGenerateRAM \$((\${GALAXY_MEMORY_MB:-31000} * 1000000))
5
f5eb9afa8f8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 9b68f6ae375aed38493f8399b8572347c750336d
iuc
parents: 4
diff changeset
125 &&
f5eb9afa8f8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 9b68f6ae375aed38493f8399b8572347c750336d
iuc
parents: 4
diff changeset
126 #end if
f5eb9afa8f8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 9b68f6ae375aed38493f8399b8572347c750336d
iuc
parents: 4
diff changeset
127 ]]></token>
6
64deddb6a8ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 57f71aa633a43ab02bbf05acd0c6d7f406e01f1e"
iuc
parents: 5
diff changeset
128 <token name="@REFGENOMEHANDLING@" ><![CDATA[
5
f5eb9afa8f8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 9b68f6ae375aed38493f8399b8572347c750336d
iuc
parents: 4
diff changeset
129 --runThreadN \${GALAXY_SLOTS:-4}
f5eb9afa8f8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 9b68f6ae375aed38493f8399b8572347c750336d
iuc
parents: 4
diff changeset
130 --genomeLoad NoSharedMemory
f5eb9afa8f8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 9b68f6ae375aed38493f8399b8572347c750336d
iuc
parents: 4
diff changeset
131 --genomeDir
f5eb9afa8f8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 9b68f6ae375aed38493f8399b8572347c750336d
iuc
parents: 4
diff changeset
132 #if str($refGenomeSource.geneSource) == 'history':
f5eb9afa8f8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 9b68f6ae375aed38493f8399b8572347c750336d
iuc
parents: 4
diff changeset
133 tempstargenomedir
f5eb9afa8f8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 9b68f6ae375aed38493f8399b8572347c750336d
iuc
parents: 4
diff changeset
134 #else:
f5eb9afa8f8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 9b68f6ae375aed38493f8399b8572347c750336d
iuc
parents: 4
diff changeset
135 '${refGenomeSource.GTFconditional.genomeDir.fields.path}'
f5eb9afa8f8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 9b68f6ae375aed38493f8399b8572347c750336d
iuc
parents: 4
diff changeset
136 ## Handle difference between indices with/without annotations
10
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
137 #if str($refGenomeSource.GTFconditional.GTFselect) == 'without-gtf-with-gtf':
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
138 --sjdbOverhang $refGenomeSource.GTFconditional.sjdbOverhang
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
139 --sjdbGTFfile '${refGenomeSource.GTFconditional.sjdbGTFfile}'
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
140 #if str($refGenomeSource.GTFconditional.sjdbGTFfile.ext) == 'gff3':
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
141 --sjdbGTFtagExonParentTranscript Parent
5
f5eb9afa8f8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 9b68f6ae375aed38493f8399b8572347c750336d
iuc
parents: 4
diff changeset
142 #end if
f5eb9afa8f8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 9b68f6ae375aed38493f8399b8572347c750336d
iuc
parents: 4
diff changeset
143 #end if
10
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
144 #end if
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
145 ]]></token>
9
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
146 <token name="@READSHANDLING@" ><![CDATA[
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
147 ## Check that the input pairs are of the same type
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
148 ## otherwise STARsolo will run for a long time and then error out.
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
149 ## We consume either repeats of two inputs R1 + R2
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
150 ## or a collection of paired reads.
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
151 #if str($sc.input_types.use) == "repeat":
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
152 #set $reads1 = []
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
153 #set $reads2 = []
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
154 #for $r1, $r2 in zip($sc.input_types.input1, $sc.input_types.input2):
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
155 #assert $r1.datatype == $r2.datatype
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
156 #silent $reads1.append(str($r1))
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
157 #silent $reads2.append(str($r2))
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
158 #end for
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
159 #set $reads1 = ','.join($reads1)
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
160 #set $reads2 = ','.join($reads2)
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
161 #elif str($sc.input_types.use) == "list_paired":
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
162 #set $r1 = $sc.input_types.input_collection.forward
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
163 #set $r2 = $sc.input_types.input_collection.reverse
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
164 #set $reads1 = $r1
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
165 #set $reads2 = $r2
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
166 #end if
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
167 ## cDNA sequence(s) [R2] always go first, then barcode(s) [R1]
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
168 ## see: Section 3.2 of STAR manual for multiple inputs, and Section 13 for STARsolo inputs
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
169 --readFilesIn $reads2 $reads1
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
170 --soloCBmatchWLtype $sc.soloCBmatchWLtype
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
171 #if $r1.is_of_type('fastq.gz', 'fastqsanger.gz'):
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
172 @FASTQ_GZ_OPTION@
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
173 #end if
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
174 ]]></token>
10
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
175 <token name="@LIMITS@" ><![CDATA[
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
176 --limitOutSJoneRead $getVar('algo.params.junction_limits.limitOutSJoneRead', $getVar('solo.junction_limits.limitOutSJoneRead', 1000))
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
177 --limitOutSJcollapsed $getVar('algo.params.junction_limits.limitOutSJcollapsed', $getVar('solo.junction_limits.limitOutSJcollapsed', 1000000))
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
178 --limitSjdbInsertNsj $getVar('algo.params.junction_limits.limitSjdbInsertNsj', $getVar('solo.junction_limits.limitSjdbInsertNsj', 1000000))
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
179 ]]></token>
7
6c6c6df09e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 6
diff changeset
180 <xml name="ref_selection">
10
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
181 <param argument="--genomeFastaFiles" type="data" format="fasta,fasta.gz" label="Select a reference genome" />
9
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
182 <param argument="--genomeSAindexNbases" type="integer" min="2" max="16" value="14" label="Length of the SA pre-indexing string" help="Typically between 10 and 15. Longer strings will use much more memory, but allow faster searches. For small genomes, the parameter --genomeSAindexNbases must be scaled down to min(14, log2(GenomeLength)/2 - 1)"/>
7
6c6c6df09e64 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 6
diff changeset
183 </xml>
5
f5eb9afa8f8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 9b68f6ae375aed38493f8399b8572347c750336d
iuc
parents: 4
diff changeset
184 <xml name="stdio" >
f5eb9afa8f8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 9b68f6ae375aed38493f8399b8572347c750336d
iuc
parents: 4
diff changeset
185 <stdio>
f5eb9afa8f8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 9b68f6ae375aed38493f8399b8572347c750336d
iuc
parents: 4
diff changeset
186 <regex match="FATAL error" source="both" level="fatal"/>
f5eb9afa8f8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 9b68f6ae375aed38493f8399b8572347c750336d
iuc
parents: 4
diff changeset
187 <regex match="EXITING: FATAL INPUT ERROR:" source="both" level="fatal"/>
f5eb9afa8f8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 9b68f6ae375aed38493f8399b8572347c750336d
iuc
parents: 4
diff changeset
188 <regex match="EXITING: fatal error trying to allocate genome arrays, exception thrown: std::bad_alloc" source="both" level="fatal"/>
f5eb9afa8f8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 9b68f6ae375aed38493f8399b8572347c750336d
iuc
parents: 4
diff changeset
189 <regex match="\[sam_read1\] missing header\? Abort!" source="both" level="fatal"/>
6
64deddb6a8ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 57f71aa633a43ab02bbf05acd0c6d7f406e01f1e"
iuc
parents: 5
diff changeset
190 <yield />
5
f5eb9afa8f8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 9b68f6ae375aed38493f8399b8572347c750336d
iuc
parents: 4
diff changeset
191 </stdio>
f5eb9afa8f8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 9b68f6ae375aed38493f8399b8572347c750336d
iuc
parents: 4
diff changeset
192 </xml>
9
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
193 <xml name="input_selection">
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
194 <conditional name="input_types" >
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
195 <param name="use" type="select" label="Input Type" >
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
196 <option value="repeat" >Separate barcode and cDNA reads</option>
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
197 <option value="list_paired" >Paired collection of barcode and cDNA reads</option>
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
198 </param>
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
199 <when value="repeat">
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
200 <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input1" type="data" multiple="true"
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
201 label="RNA-Seq FASTQ/FASTA file, Barcode reads" />
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
202 <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input2" type="data" multiple="true"
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
203 label="RNA-Seq FASTQ/FASTA file, cDNA reads"/>
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
204 </when>
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
205 <when value="list_paired">
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
206 <param name="input_collection" collection_type="paired" type="data_collection" format="fastq,fasta,fastq.gz,fastqsanger.gz" label="Collection of Pairs" />
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
207 </when>
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
208 </conditional>
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
209 </xml>
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
210 <xml name="input_selection_smart_seq">
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
211 <conditional name="input_types_smart_seq" >
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
212 <param name="use" type="select" label="Input Type" >
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
213 <option value="list_single_end" >Single-end FASTQ collection</option>
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
214 <option value="list_paired_end" >Paired FASTQ collection</option>
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
215 </param>
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
216 <when value="list_single_end">
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
217 <param name="single_end_collection" collection_type="list" type="data_collection" format="fastq,fasta,fastq.gz,fastqsanger.gz" label="List of single-end FASTQ files" />
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
218 </when>
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
219 <when value="list_paired_end">
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
220 <param name="paired_end_collection" collection_type="list:paired" type="data_collection" format="fastq,fasta,fastq.gz,fastqsanger.gz" label="List of paired-end FASTQ files" />
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
221 </when>
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
222 </conditional>
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
223 </xml>
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
224 <xml name="umidedup_options">
11
d63c1442407f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 096286097ed5cdf189a1b68c3fc34d10f4142e54
iuc
parents: 10
diff changeset
225 <option value="1MM_All" selected="true">Collapse all UMIs with 1 mismatch distance to each other (1MM_All)</option>
9
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
226 <option value="1MM_Directional_UMItools" >Directional method from the UMI-tool</option>
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
227 <option value="1MM_Directional" >Directional with stringent UMI deduplication</option>
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
228 </xml>
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
229 <xml name="anchor_types">
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
230 <option value="0">Read start</option>
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
231 <option value="1">Read end</option>
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
232 <option value="2">Adapter start</option>
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
233 <option value="3">Adapter end</option>
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
234 </xml>
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
235 <xml name="cb_match_wl_common">
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
236 <option value="Exact" >Exact</option>
11
d63c1442407f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 096286097ed5cdf189a1b68c3fc34d10f4142e54
iuc
parents: 10
diff changeset
237 <option value="1MM" >Single match (1MM)</option>
9
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
238 </xml>
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
239 <xml name="cb_match_wl_cellranger">
11
d63c1442407f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 096286097ed5cdf189a1b68c3fc34d10f4142e54
iuc
parents: 10
diff changeset
240 <option value="1MM_multi" selected="true" >Multiple matches (CellRanger 2, 1MM_multi)</option>
d63c1442407f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 096286097ed5cdf189a1b68c3fc34d10f4142e54
iuc
parents: 10
diff changeset
241 <option value="1MM_multi_pseudocounts" >Multiple matches (CellRanger 3, 1MM_multi_pseudocounts)</option>
d63c1442407f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 096286097ed5cdf189a1b68c3fc34d10f4142e54
iuc
parents: 10
diff changeset
242 <option value="1MM_multi_Nbase_pseudocounts" >Multimatching to WL is allowed for CBs with N-bases (CellRanger 3, 1MM_multi_Nbase_pseudocounts)</option>
9
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
243 </xml>
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
244 <xml name="solo_adapter_params">
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
245 <param argument="--soloAdapterSequence" type="text" value="-" label="Adapter sequence to anchor barcodes." >
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
246 <sanitizer>
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
247 <valid initial="string.digits">
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
248 <add value="-"/>
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
249 <add value="A"/>
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
250 <add value="T"/>
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
251 <add value="C"/>
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
252 <add value="G"/>
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
253 <add value="N"/>
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
254 </valid>
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
255 </sanitizer>
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
256 </param>
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
257 <param argument="--soloAdapterMismatchesNmax" type="integer" min="1" value="1" label="Maximum number of mismatches allowed in adapter sequence" />
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
258 <param argument="--clipAdapterType" type="select" >
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
259 <option value="Hamming" selected="true" >Adapter clipping based on Hamming distance</option>
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
260 <option value="CellRanger4" >5p and 3p adapter clipping similar to CellRanger4</option>
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
261 <option value="None" >No adapter clipping</option>
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
262 </param>
c520a52b5174 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
iuc
parents: 7
diff changeset
263 </xml>
10
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
264 <xml name="common_SAM_attributes">
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
265 <option value="NH" selected="true">NH (number of reported alignments/hits for the read)</option>
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
266 <option value="HI" selected="true">HI (query hit index)</option>
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
267 <option value="AS" selected="true">AS (local alignment score)</option>
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
268 <option value="nM" selected="true">nM (number of mismatches per (paired) alignment)</option>
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
269 <option value="NM">NM (edit distance of the aligned read to the reference)</option>
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
270 <option value="MD">MD (string for mismatching positions)</option>
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
271 <option value="jM">jM (intron motifs for all junctions)</option>
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
272 <option value="jI">jI (1-based start and end of introns for all junctions)</option>
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
273 </xml>
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
274 <xml name="limits">
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
275 <section name="junction_limits" title="Junction Limits" expanded="false">
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
276 <param argument="--limitOutSJoneRead" type="integer" min="1" value="1000" label="Maximum number of junctions for one read (including all multimappers)" />
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
277 <param argument="--limitOutSJcollapsed" type="integer" min="1" value="1000000" label="Maximum number of collapsed junctions" />
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
278 <param argument="--limitSjdbInsertNsj" type="integer" min="0" value="1000000" label="Maximum number of inserts to be inserted into the genome on the fly." />
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
279 </section>
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
280 </xml>
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
281 <xml name="outCountActions">
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
282 <actions>
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
283 <action name="column_names" type="metadata" default="GeneID,Counts_unstrand,Counts_firstStrand,Counts_secondStrand" />
11
d63c1442407f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 096286097ed5cdf189a1b68c3fc34d10f4142e54
iuc
parents: 10
diff changeset
284 <expand macro="dbKeyAction"/>
10
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
285 </actions>
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
286 </xml>
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
287 <xml name="outWig">
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
288 <conditional name="outWig">
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
289 <param name="outWigType" type="select" label="Compute coverage">
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
290 <option value="None">No coverage</option>
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
291 <option value="bedGraph">Yes in bedgraph format</option>
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
292 <option value="wiggle">Yes in wiggle format</option>
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
293 </param>
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
294 <when value="None">
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
295 <!-- This is necessary for the filtering of output -->
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
296 <param name="outWigStrand" type="hidden" value="false" />
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
297 </when>
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
298 <when value="bedGraph">
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
299 <expand macro="outWigParams"/>
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
300 </when>
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
301 <when value="wiggle">
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
302 <expand macro="outWigParams"/>
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
303 </when>
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
304 </conditional>
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
305 </xml>
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
306 <xml name="outWigParams">
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
307 <param name="outWigTypeSecondWord" type="select" label="Input for coverage">
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
308 <option value="">Default (everything that mapped)</option>
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
309 <option value="read_5p">signal from only 5’ of the 1st read</option>
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
310 <option value="read2">signal from only 2nd read</option>
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
311 </param>
11
d63c1442407f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 096286097ed5cdf189a1b68c3fc34d10f4142e54
iuc
parents: 10
diff changeset
312 <param argument="--outWigStrand" type="boolean" truevalue="Stranded" falsevalue="Unstranded" checked="true" label="Generate a coverage for each strand (stranded coverage)"/>
10
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
313 <param argument="--outWigReferencesPrefix" type="text" value="-" label="prefix matching reference name" help="For example, set 'chr' if you mapped on an ensembl genome but you want to display on UCSC"/>
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
314 <param argument="--outWigNorm" type="boolean" truevalue="RPM" falsevalue="None" checked="true" label="Normalize coverage to million of mapped reads (RPM)"/>
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
315 </xml>
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
316 <token name="@OUTWIG@"><![CDATA[
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
317 #if str($outWig.outWigType) != 'None':
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
318 --outWigType '$outWig.outWigType' '$outWig.outWigTypeSecondWord'
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
319 --outWigStrand '$outWig.outWigStrand'
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
320 --outWigReferencesPrefix '$outWig.outWigReferencesPrefix'
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
321 --outWigNorm '$outWig.outWigNorm'
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
322 #end if
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
323 ]]></token>
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
324 <token name="@OUTWIGOUTPUTS@"><![CDATA[
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
325 #if str($outWig.outWigType) == "bedGraph":
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
326 && mv Signal.Unique.str1.out.bg Signal.Unique.str1.out
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
327 && mv Signal.UniqueMultiple.str1.out.bg Signal.UniqueMultiple.str1.out
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
328 #if str($outWig.outWigStrand) == "Stranded":
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
329 && mv Signal.Unique.str2.out.bg Signal.Unique.str2.out
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
330 && mv Signal.UniqueMultiple.str2.out.bg Signal.UniqueMultiple.str2.out
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
331 #end if
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
332 #elif str($outWig.outWigType) == "wiggle":
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
333 && mv Signal.Unique.str1.out.wig Signal.Unique.str1.out
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
334 && mv Signal.UniqueMultiple.str1.out.wig Signal.UniqueMultiple.str1.out
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
335 #if str($outWig.outWigStrand) == "Stranded":
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
336 && mv Signal.Unique.str2.out.wig Signal.Unique.str2.out
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
337 && mv Signal.UniqueMultiple.str2.out.wig Signal.UniqueMultiple.str2.out
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
338 #end if
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
339 #end if
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
340 ]]></token>
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
341 <xml name="outWigOutputs">
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
342 <data format="bedgraph" name="signal_unique_str1" label="${tool.name} on ${on_string}: Coverage Uniquely mapped strand 1" from_work_dir="Signal.Unique.str1.out">
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
343 <filter>outWig['outWigType'] != "None"</filter>
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
344 <expand macro="dbKeyActions" />
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
345 <change_format>
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
346 <when input="outWig.outWigType" value="wiggle" format="wig" />
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
347 </change_format>
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
348 </data>
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
349 <data format="bedgraph" name="signal_uniquemultiple_str1" label="${tool.name} on ${on_string}: Coverage Uniquely + Multiple mapped strand 1" from_work_dir="Signal.UniqueMultiple.str1.out">
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
350 <filter>outWig['outWigType'] != "None"</filter>
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
351 <expand macro="dbKeyActions" />
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
352 <change_format>
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
353 <when input="outWig.outWigType" value="wiggle" format="wig" />
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
354 </change_format>
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
355 </data>
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
356 <data format="bedgraph" name="signal_unique_str2" label="${tool.name} on ${on_string}: Coverage Uniquely mapped strand 2" from_work_dir="Signal.Unique.str2.out">
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
357 <filter>outWig['outWigType'] != "None" and outWig['outWigStrand']</filter>
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
358 <expand macro="dbKeyActions" />
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
359 <change_format>
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
360 <when input="outWig.outWigType" value="wiggle" format="wig" />
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
361 </change_format>
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
362 </data>
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
363 <data format="bedgraph" name="signal_uniquemultiple_str2" label="${tool.name} on ${on_string}: Coverage Uniquely + Multiple mapped strand 2" from_work_dir="Signal.UniqueMultiple.str2.out">
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
364 <filter>outWig['outWigType'] != "None" and outWig['outWigStrand']</filter>
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
365 <expand macro="dbKeyActions" />
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
366 <change_format>
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
367 <when input="outWig.outWigType" value="wiggle" format="wig" />
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
368 </change_format>
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
369 </data>
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
370 </xml>
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
371 <xml name="quantMode">
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
372 <conditional name="quantmode_output">
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
373 <param argument="--quantMode" type="select"
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
374 label="Per gene/transcript output"
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
375 help="STAR can provide analysis results not only with respect to the reference genome, but also with respect to genes and transcripts described by a gene model. Note: This functionality requires either the selection above of a cached index with a gene model, or a gene model provided alongside the index/reference genome in GTF or GFF3 format!">
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
376 <option value="-">No per gene or transcript output</option>
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
377 <option value="GeneCounts">Per gene read counts (GeneCounts)</option>
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
378 <option value="TranscriptomeSAM">Transcript-based BAM output (TranscriptomeSAM)</option>
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
379 <option value="TranscriptomeSAM GeneCounts">Both per gene read counts and transcript-based BAM output (TranscriptomeSAM GeneCounts)</option>
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
380 </param>
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
381 <when value="-" />
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
382 <when value="GeneCounts" />
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
383 <when value="TranscriptomeSAM">
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
384 <param argument="--quantTranscriptomeBan" type="boolean" truevalue="IndelSoftclipSingleend" falsevalue="Singleend"
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
385 label="Exclude alignments with indels or soft clipping from the transcriptome BAM output?"
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
386 help="You will need to exclude alignments with indels and soft-clipped bases from the transcriptome BAM output for compatibility with certain transcript quantification tools, most notably RSEM. If you are using a tool, like eXpress, that can deal with indels and soft-clipped bases, you can achieve better results by leaving this option disabled." />
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
387 </when>
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
388 <when value="TranscriptomeSAM GeneCounts">
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
389 <param argument="--quantTranscriptomeBan" type="boolean" truevalue="IndelSoftclipSingleend" falsevalue="Singleend"
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
390 label="Exclude alignments with indels or soft clipping from the transcriptome BAM output?"
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
391 help="You will need to exclude alignments with indels and soft-clipped bases from the transcriptome BAM output for compatibility with certain transcript quantification tools, most notably RSEM. If you are using a tool, like eXpress, that can deal with indels and soft-clipped bases, you can achieve better results by leaving this option disabled." />
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
392 </when>
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
393 </conditional>
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
394 </xml>
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
395 <xml name="quantModeNoGTF">
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
396 <conditional name="quantmode_output">
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
397 <param argument="--quantMode" type="select"
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
398 label="Per gene/transcript output">
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
399 <option value="-">No per gene or transcript output as no GTF was provided</option>
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
400 </param>
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
401 <when value="-" />
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
402 </conditional>
a225487bf618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents: 9
diff changeset
403 </xml>
11
d63c1442407f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 096286097ed5cdf189a1b68c3fc34d10f4142e54
iuc
parents: 10
diff changeset
404 <xml name="outSAMmapqUnique">
d63c1442407f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 096286097ed5cdf189a1b68c3fc34d10f4142e54
iuc
parents: 10
diff changeset
405 <!-- MAPQ 255 is the default in STAR (coming from tophat behaviour and compatibility for Cufflinks) but it is a problematic value
d63c1442407f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 096286097ed5cdf189a1b68c3fc34d10f4142e54
iuc
parents: 10
diff changeset
406 - according to SAM/BAM specs it means "undefined".
d63c1442407f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 096286097ed5cdf189a1b68c3fc34d10f4142e54
iuc
parents: 10
diff changeset
407 - Using 255 as the max mapq causes problem with modern downstream tools like mutect2: https://sites.duke.edu/workblog/2021/08/18/star-rnaseq-gatk-mutect2/ and 60 has become an inofficial replacement for 255. -->
d63c1442407f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 096286097ed5cdf189a1b68c3fc34d10f4142e54
iuc
parents: 10
diff changeset
408 <param argument="--outSAMmapqUnique" type="integer" value="60" min="0" max="255"
d63c1442407f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 096286097ed5cdf189a1b68c3fc34d10f4142e54
iuc
parents: 10
diff changeset
409 label="MAPQ value for unique mappers"
d63c1442407f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 096286097ed5cdf189a1b68c3fc34d10f4142e54
iuc
parents: 10
diff changeset
410 help="STAR bases the mapping quality scores of alignment records in its BAM output on the number of alternative mappings for the read. If a read maps to multiple locations on the reference genome, the following MAPQ scoring scheme is
d63c1442407f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 096286097ed5cdf189a1b68c3fc34d10f4142e54
iuc
parents: 10
diff changeset
411 used: >=5 mappings => MAPQ=0; 3-4 mappings => MAPQ=1; 2 mappings => MAPQ=3. This setting lets you control the MAPQ used for reads mapped to a single location. Set to 255 for compatibility with Cufflink (default in STAR) but keep to 60 for modern downstream tools like mutect2." />
d63c1442407f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 096286097ed5cdf189a1b68c3fc34d10f4142e54
iuc
parents: 10
diff changeset
412 </xml>
1
cdc4d8a998e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
diff changeset
413 </macros>