Mercurial > repos > yhoogstrate > crossmap

annotate crossmap.xml @ 35:9a3254bb8c4e draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 2a0f8a26551929e52f6aea1d109b8a3bda81af8b-dirty
author yhoogstrate
date Thu, 12 Nov 2015 16:08:34 -0500
parents 5500eeb65605
children 47d4f148eb8c
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
28
f1fa5c4eba47 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3d455a19e1a217e8a8f07784892d4a521c18fc10-dirty
yhoogstrate
parents: 26
diff changeset
1 <tool id="crossmap" name="CrossMap" version="0.2.d">
1
f252cf28746d Uploaded
yhoogstrate
parents:
diff changeset
2 <description>Convert genome coordinates or annotation files between genome assemblies</description>
f252cf28746d Uploaded
yhoogstrate
parents:
diff changeset
3
f252cf28746d Uploaded
yhoogstrate
parents:
diff changeset
4 <requirements>
26
a366e3148677 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 6e66f1e17650f888c84ec82d100195db61dffdc7-dirty
yhoogstrate
parents: 24
diff changeset
5 <requirement type="package" version="312">ucsc_tools</requirement>
23
b55865ba56c8 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 290b453ad2abdb65322ec2e50889aaf2b03bb095-dirty
yhoogstrate
parents: 20
diff changeset
6 <requirement type="package" version="2.7">python</requirement>
13
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
7 <requirement type="package" version="0.2">crossmap</requirement>
1
f252cf28746d Uploaded
yhoogstrate
parents:
diff changeset
8 </requirements>
f252cf28746d Uploaded
yhoogstrate
parents:
diff changeset
9
8
9750f8c1d3cb planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a-dirty
yhoogstrate
parents: 5
diff changeset
10 <stdio>
11
a5eb1023fc34 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 0acafcc4ce1261ec93eee1ad209a05246f4f02fd-dirty
yhoogstrate
parents: 9
diff changeset
11 <regex match="Usage: CrossMap.py" source="stdout" level="fatal"/>
13
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
12 <regex match=".*" source="both" level="log"/>
8
9750f8c1d3cb planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a-dirty
yhoogstrate
parents: 5
diff changeset
13 </stdio>
16
263581d4dd90 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 74570ff45544cfe08ef65d0b712f8d44da6f545c
yhoogstrate
parents: 13
diff changeset
14
29
871455bebf64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 28
diff changeset
15 <version_command>python $CROSSMAP_ROOT_DIR/bin/CrossMap.py 2&gt;&amp;1 | head -n 1 | grep -E --only-matching 'CrossMap.*'</version_command>
16
263581d4dd90 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 74570ff45544cfe08ef65d0b712f8d44da6f545c
yhoogstrate
parents: 13
diff changeset
16
35
9a3254bb8c4e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 2a0f8a26551929e52f6aea1d109b8a3bda81af8b-dirty
yhoogstrate
parents: 33
diff changeset
17 <!-- First line of CrossMap has hardcoded "#!/usr/bin/python". This makes use of Galaxy's python: -->
9a3254bb8c4e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 2a0f8a26551929e52f6aea1d109b8a3bda81af8b-dirty
yhoogstrate
parents: 33
diff changeset
18 <command><![CDATA[
28
f1fa5c4eba47 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3d455a19e1a217e8a8f07784892d4a521c18fc10-dirty
yhoogstrate
parents: 26
diff changeset
19 python \$CROSSMAP_ROOT_DIR/bin/CrossMap.py
31
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
20 ${multiple.input_format.replace("sam","bam")}
5
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a
yhoogstrate
parents: 1
diff changeset
21
31
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
22 #if $multiple.input_format == "vcf" and $multiple.seq_source.index_source == "cached"
5
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a
yhoogstrate
parents: 1
diff changeset
23 <!-- This is the 2nd dbkey, and the corresponding value has to be looked up -->
31
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
24 "${filter(lambda x: str( x[1] ) == str($multiple.seq_source.input_chain ), $__app__.tool_data_tables['liftOver'].get_fields())[0][2] }"
5
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a
yhoogstrate
parents: 1
diff changeset
25 #else
31
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
26 "$multiple.seq_source.input_chain"
5
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a
yhoogstrate
parents: 1
diff changeset
27 #end if
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a
yhoogstrate
parents: 1
diff changeset
28
31
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
29 #if $multiple.input_format in ["bam", "sam"]
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
30 -m $multiple.insert_size
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
31 -s $multiple.insert_size_stdev
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
32 -t $multiple.insert_size_fold
5
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a
yhoogstrate
parents: 1
diff changeset
33 #end if
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a
yhoogstrate
parents: 1
diff changeset
34
31
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
35 "$multiple.seq_source.input"
5
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a
yhoogstrate
parents: 1
diff changeset
36
31
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
37 #if $multiple.input_format == "vcf"
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
38 "$multiple.seq_source.input_fasta"
5
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a
yhoogstrate
parents: 1
diff changeset
39 #end if
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a
yhoogstrate
parents: 1
diff changeset
40
31
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
41 #if str($multiple.include_fails) == "True"
11
a5eb1023fc34 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 0acafcc4ce1261ec93eee1ad209a05246f4f02fd-dirty
yhoogstrate
parents: 9
diff changeset
42 >
a5eb1023fc34 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 0acafcc4ce1261ec93eee1ad209a05246f4f02fd-dirty
yhoogstrate
parents: 9
diff changeset
43 #end if
9
0cae6e3273a8 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 0acafcc4ce1261ec93eee1ad209a05246f4f02fd
yhoogstrate
parents: 8
diff changeset
44
11
a5eb1023fc34 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 0acafcc4ce1261ec93eee1ad209a05246f4f02fd-dirty
yhoogstrate
parents: 9
diff changeset
45 "$output"
13
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
46
31
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
47 #if $multiple.input_format in ["bam", "sam"]
33
5500eeb65605 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit dc4deb40aeefdf8b20f496626fe0ba28cbe248ed
yhoogstrate
parents: 32
diff changeset
48 && mv "${output}.${multiple.input_format}" "$output"
5500eeb65605 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit dc4deb40aeefdf8b20f496626fe0ba28cbe248ed
yhoogstrate
parents: 32
diff changeset
49 && mv "${output}.unmap.${multiple.input_format}" "$output_unmapped"
31
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
50 #else if $multiple.input_format in ["vcf"]
33
5500eeb65605 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit dc4deb40aeefdf8b20f496626fe0ba28cbe248ed
yhoogstrate
parents: 32
diff changeset
51 && mv "${output}" "$output"
5500eeb65605 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit dc4deb40aeefdf8b20f496626fe0ba28cbe248ed
yhoogstrate
parents: 32
diff changeset
52 && mv "${output}.unmap" "$output_unmapped"
31
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
53 #else if $multiple.input_format in ["wig", "bigwig"]
33
5500eeb65605 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit dc4deb40aeefdf8b20f496626fe0ba28cbe248ed
yhoogstrate
parents: 32
diff changeset
54 && mv "${output}.bw" "$output"
5500eeb65605 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit dc4deb40aeefdf8b20f496626fe0ba28cbe248ed
yhoogstrate
parents: 32
diff changeset
55 && mv "${output}.sorted.bgr" "$output2"
13
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
56 #end if
35
9a3254bb8c4e planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 2a0f8a26551929e52f6aea1d109b8a3bda81af8b-dirty
yhoogstrate
parents: 33
diff changeset
57 ]]></command>
1
f252cf28746d Uploaded
yhoogstrate
parents:
diff changeset
58
f252cf28746d Uploaded
yhoogstrate
parents:
diff changeset
59 <inputs>
31
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
60 <conditional name="multiple">
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
61 <param name="input_format" type="select" label="Convert a file of the following format">
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
62 <option value="bam">BAM</option>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
63 <option value="sam">SAM</option>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
64 <option value="bed">BED or BED-like</option>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
65 <option value="bigwig">BigWig</option>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
66 <option value="gff">GFF or GTF</option>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
67 <option value="vcf">VCF</option>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
68 <option value="wig">Wiggle or bedGraph</option>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
69 </param>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
70 <when value="bam">
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
71 <conditional name="seq_source">
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
72 <param name="index_source" type="select" label="Source for LiftOver Data (chain file)">
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
73 <option value="cached">Local data (in galaxy)</option>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
74 <option value="history">From History</option>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
75 </param>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
76 <when value="cached">
33
5500eeb65605 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit dc4deb40aeefdf8b20f496626fe0ba28cbe248ed
yhoogstrate
parents: 32
diff changeset
77 <param type="data" format="bam" name="input" label="BAM file">
31
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
78 <validator type="unspecified_build" />
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
79 <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build." />
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
80 </param>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
81 <param name="input_chain" type="select" label="Lift Over To">
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
82 <options from_file="liftOver.loc">
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
83 <column name="name" index="1"/>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
84 <column name="value" index="2"/>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
85 <column name="dbkey" index="0"/>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
86 <filter type="data_meta" ref="input" key="dbkey" column="0" />
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
87 </options>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
88 </param>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
89 </when>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
90 <when value="history">
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
91 <param type="data" format="bam,sam" name="input" label="BAM/SAM file" />
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
92 <param type="data" format="csv" name="input_chain" label="LiftOver chain file" />
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
93 </when>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
94 </conditional>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
95
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
96 <param name="insert_size" type="float" value="200.0" label="Insert size (-m)" help="Average insert size of pair-end sequencing (bp) [default=200.0]" />
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
97 <param name="insert_size_stdev" type="float" value="30.0" label="Insert size std. dev (-s)" help="Stanadard deviation of insert size. [default=30.0]" />
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
98 <param name="insert_size_fold" type="float" value="3.0" label="Insert size std. dev foldchange (-t)" help="A mapped pair is considered as 'proper pair' if both ends mapped to different strand and the distance between them is less then '-t' * stdev from the mean. [default=3.0]" />
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
99
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
100 <param name="include_fails" type="hidden" tvalue="False" />
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
101 </when>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
102 <when value="sam"><!-- BAM and SAM are exactly the same conditions, but they need to be separate to get the proper output format -->
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
103 <conditional name="seq_source">
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
104 <param name="index_source" type="select" label="Source for LiftOver Data (chain file)">
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
105 <option value="cached">Local data (in galaxy)</option>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
106 <option value="history">From History</option>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
107 </param>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
108 <when value="cached">
33
5500eeb65605 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit dc4deb40aeefdf8b20f496626fe0ba28cbe248ed
yhoogstrate
parents: 32
diff changeset
109 <param type="data" format="sam" name="input" label="SAM file">
31
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
110 <validator type="unspecified_build" />
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
111 <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build." />
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
112 </param>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
113 <param name="input_chain" type="select" label="Lift Over To">
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
114 <options from_file="liftOver.loc">
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
115 <column name="name" index="1"/>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
116 <column name="value" index="2"/>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
117 <column name="dbkey" index="0"/>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
118 <filter type="data_meta" ref="input" key="dbkey" column="0" />
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
119 </options>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
120 </param>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
121 </when>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
122 <when value="history">
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
123 <param type="data" format="bam,sam" name="input" label="BAM/SAM file" />
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
124 <param type="data" format="csv" name="input_chain" label="LiftOver chain file" />
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
125 </when>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
126 </conditional>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
127
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
128 <param name="insert_size" type="float" value="200.0" label="Insert size (-m)" help="Average insert size of pair-end sequencing (bp) [default=200.0]" />
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
129 <param name="insert_size_stdev" type="float" value="30.0" label="Insert size std. dev (-s)" help="Stanadard deviation of insert size. [default=30.0]" />
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
130 <param name="insert_size_fold" type="float" value="3.0" label="Insert size std. dev foldchange (-t)" help="A mapped pair is considered as 'proper pair' if both ends mapped to different strand and the distance between them is less then '-t' * stdev from the mean. [default=3.0]" />
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
131
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
132 <param name="include_fails" type="hidden" tvalue="False" />
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
133 </when>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
134 <when value="bed">
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
135 <conditional name="seq_source">
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
136 <param name="index_source" type="select" label="Source for LiftOver Data (chain file)">
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
137 <option value="cached">Local data (in galaxy)</option>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
138 <option value="history">From History</option>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
139 </param>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
140 <when value="cached">
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
141 <param format="bed" name="input" type="data" label="BED file" help="BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns.">
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
142 <validator type="unspecified_build" />
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
143 <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build." />
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
144 </param>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
145 <param name="input_chain" type="select" label="Lift Over To">
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
146 <options from_file="liftOver.loc">
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
147 <column name="name" index="1"/>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
148 <column name="value" index="2"/>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
149 <column name="dbkey" index="0"/>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
150 <filter type="data_meta" ref="input" key="dbkey" column="0" />
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
151 </options>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
152 </param>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
153 </when>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
154 <when value="history">
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
155 <param type="data" format="bed" name="input" label="BED file" help="BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns." />
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
156 <param type="data" format="csv" name="input_chain" label="LiftOver chain file" />
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
157 </when>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
158 </conditional>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
159
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
160 <param name="include_fails" type="boolean" truevalue="True" checked="false" falsevalue="False" label="Include failed liftovers" help="If a coordinate can not be lift over, do you want to include it in the output (it is still being marked 'fail')" />
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
161 </when>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
162 <when value="bigwig">
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
163 <conditional name="seq_source">
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
164 <param name="index_source" type="select" label="Source for LiftOver Data (chain file)">
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
165 <option value="cached">Local data (in galaxy)</option>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
166 <option value="history">From History</option>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
167 </param>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
168 <when value="cached">
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
169 <param format="bigwig" name="input" type="data" label="BigWig file">
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
170 <validator type="unspecified_build" />
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
171 <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build." />
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
172 </param>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
173 <param name="input_chain" type="select" label="Lift Over To">
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
174 <options from_file="liftOver.loc">
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
175 <column name="name" index="1"/>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
176 <column name="value" index="2"/>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
177 <column name="dbkey" index="0"/>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
178 <filter type="data_meta" ref="input" key="dbkey" column="0" />
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
179 </options>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
180 </param>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
181 </when>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
182 <when value="history">
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
183 <param type="data" format="bigwig" name="input" label="BigWig file" />
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
184 <param type="data" format="csv" name="input_chain" label="LiftOver chain file" />
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
185 </when>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
186 </conditional>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
187
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
188 <param name="include_fails" type="hidden" tvalue="False" />
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
189 </when>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
190 <when value="gff">
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
191 <conditional name="seq_source">
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
192 <param name="index_source" type="select" label="Source for LiftOver Data (chain file)">
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
193 <option value="cached">Local data (in galaxy)</option>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
194 <option value="history">From History</option>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
195 </param>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
196 <when value="cached">
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
197 <param format="gtf,gff,gff3" name="input" type="data" label="GTF/GFF file">
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
198 <validator type="unspecified_build" />
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
199 <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build." />
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
200 </param>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
201 <param name="input_chain" type="select" label="Lift Over To">
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
202 <options from_file="liftOver.loc">
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
203 <column name="name" index="1"/>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
204 <column name="value" index="2"/>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
205 <column name="dbkey" index="0"/>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
206 <filter type="data_meta" ref="input" key="dbkey" column="0" />
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
207 </options>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
208 </param>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
209 </when>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
210 <when value="history">
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
211 <param type="data" format="gtf,gff,gff3" name="input" label="GTF/GFF file" />
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
212 <param type="data" format="csv" name="input_chain" label="LiftOver chain file" />
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
213 </when>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
214 </conditional>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
215
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
216 <param name="include_fails" type="boolean" truevalue="True" checked="false" falsevalue="False" label="Include failed liftovers" help="If a coordinate can not be lift over, do you want to include it in the output (it is still being marked 'fail')" />
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
217 </when>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
218 <when value="vcf">
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
219 <conditional name="seq_source">
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
220 <param name="index_source" type="select" label="Source for LiftOver Data">
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
221 <option value="cached">Local data (in galaxy)</option>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
222 <option value="history_chain">Chain file from History</option>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
223 <option value="history_all">Chain &amp; FASTA files from History</option>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
224 </param>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
225
13
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
226 <when value="cached">
31
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
227 <param type="data" format="vcf" name="input" label="VCF file">
13
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
228 <validator type="unspecified_build" />
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
229 <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build." />
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
230 </param>
31
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
231
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
232 <!-- automatically fetch a FASTA file from the same DBKEY as the chain file -->
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
233 <param name="input_chain" type="select" label="Lift Over To (Chain file)">
13
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
234 <options from_file="liftOver.loc">
31
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
235 <column name="name" index="1" />
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
236 <column name="value" index="1" /><!-- It is not possible to send the *.chain file as value, and obtain the 2nd dbkey as parameter via a filter -->
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
237 <column name="dbkey" index="0" />
13
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
238 <filter type="data_meta" ref="input" key="dbkey" column="0" />
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
239 </options>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
240 </param>
31
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
241
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
242 <param name="input_fasta" type="select" label="Lift Over To (FASTA file)" help="The FASTA file must be on the same build (dbkey) as the LiftOver chain file">
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
243 <options from_file="all_fasta.loc">
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
244 <column name="name" index="2"/>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
245 <column name="value" index="3"/>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
246 <column name="dbkey" index="1"/>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
247 <filter type="param_value" ref="input_chain" column="1" />
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
248 </options>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
249 </param>
13
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
250 </when>
31
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
251
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
252 <when value="history_chain">
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
253 <param type="data" format="vcf" name="input" label="VCF file">
13
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
254 <validator type="unspecified_build" />
31
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
255 <validator type="dataset_metadata_in_file" filename="all_fasta.loc" metadata_name="dbkey" metadata_column="1" message="LiftOver mapping (FASTA file) is not available for the specified build." />
13
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
256 </param>
31
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
257 <param type="data" format="csv" name="input_chain" multiple="false" label="LiftOver chain file" />
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
258 <param name="input_fasta" type="select" label="Lift Over To (FASTA file)" help="The FASTA file must be on the same build (dbkey) as the LiftOver chain file">
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
259 <options from_file="all_fasta.loc">
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
260 <column name="name" index="2"/>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
261 <column name="value" index="3"/>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
262 <column name="dbkey" index="1"/>
13
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
263 </options>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
264 </param>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
265 </when>
31
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
266
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
267 <when value="history_all">
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
268 <param type="data" format="vcf" name="input" label="VCF file" />
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
269 <param type="data" format="csv" name="input_chain" multiple="false" label="LiftOver chain file" />
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
270 <param type="data" format="fasta" name="input_fasta" multiple="false" label="Full genome FASTA file" />
13
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
271 </when>
31
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
272 </conditional>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
273
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
274 <param name="include_fails" type="hidden" tvalue="False" />
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
275 </when>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
276 <when value="wig">
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
277 <conditional name="seq_source">
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
278 <param name="index_source" type="select" label="Source for LiftOver Data (chain file)">
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
279 <option value="cached">Local data (in galaxy)</option>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
280 <option value="history">From History</option>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
281 </param>
13
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
282 <when value="cached">
31
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
283 <param format="wig" name="input" type="data" label="Wiggle file">
13
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
284 <validator type="unspecified_build" />
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
285 <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build." />
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
286 </param>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
287 <param name="input_chain" type="select" label="Lift Over To">
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
288 <options from_file="liftOver.loc">
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
289 <column name="name" index="1"/>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
290 <column name="value" index="2"/>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
291 <column name="dbkey" index="0"/>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
292 <filter type="data_meta" ref="input" key="dbkey" column="0" />
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
293 </options>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
294 </param>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
295 </when>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
296 <when value="history">
31
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
297 <param format="wig" name="input" type="data" label="Wiggle file" />
13
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
298 <param type="data" format="csv" name="input_chain" label="LiftOver chain file" />
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
299 </when>
31
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
300 </conditional>
16
263581d4dd90 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 74570ff45544cfe08ef65d0b712f8d44da6f545c
yhoogstrate
parents: 13
diff changeset
301
31
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
302 <param name="include_fails" type="hidden" tvalue="False" />
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
303 </when>
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
304 </conditional>
1
f252cf28746d Uploaded
yhoogstrate
parents:
diff changeset
305 </inputs>
f252cf28746d Uploaded
yhoogstrate
parents:
diff changeset
306
f252cf28746d Uploaded
yhoogstrate
parents:
diff changeset
307 <outputs>
29
871455bebf64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 28
diff changeset
308 <data format="text" name="output" label="${tool.name} on ${on_string}">
13
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
309 <change_format>
31
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
310 <when input="multiple.input_format" value="bam" format="bam" />
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
311 <when input="multiple.input_format" value="sam" format="sam" />
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
312 <when input="multiple.input_format" value="bed" format="bed" />
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
313 <when input="multiple.input_format" value="bigwig" format="bigwig" />
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
314 <when input="multiple.input_format" value="gff" format="gff" />
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
315 <when input="multiple.input_format" value="vcf" format="vcf" />
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
316 <when input="multiple.input_format" value="wig" format="bigwig" />
13
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
317 </change_format>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
318 </data>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
319
29
871455bebf64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 28
diff changeset
320 <data format="text" name="output_unmapped" label="${tool.name} (unmapped) on ${on_string}">
32
00a4682c94bc planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 31
diff changeset
321 <filter>multiple['input_format'] in ["bam" , "vcf"]</filter>
13
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
322 <change_format>
31
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
323 <when input="multiple.input_format" value="bam" format="bam" />
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
324 <when input="multiple.input_format" value="vcf" format="vcf" />
16
263581d4dd90 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 74570ff45544cfe08ef65d0b712f8d44da6f545c
yhoogstrate
parents: 13
diff changeset
325 </change_format>
263581d4dd90 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 74570ff45544cfe08ef65d0b712f8d44da6f545c
yhoogstrate
parents: 13
diff changeset
326 </data>
29
871455bebf64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 28
diff changeset
327 <data format="text" name="output2" label="${tool.name} (bedgraph) on ${on_string}">
32
00a4682c94bc planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 31
diff changeset
328 <filter>multiple['input_format'] in ["wig"]</filter>
16
263581d4dd90 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 74570ff45544cfe08ef65d0b712f8d44da6f545c
yhoogstrate
parents: 13
diff changeset
329 <change_format>
31
ebcd672e9072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
yhoogstrate
parents: 30
diff changeset
330 <when input="multiple.input_format" value="wig" format="bedgraph" />
13
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
331 </change_format>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
332 </data>
1
f252cf28746d Uploaded
yhoogstrate
parents:
diff changeset
333 </outputs>
f252cf28746d Uploaded
yhoogstrate
parents:
diff changeset
334
f252cf28746d Uploaded
yhoogstrate
parents:
diff changeset
335 <tests>
13
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
336 <!-- BAM/SAM -->
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
337 <test>
33
5500eeb65605 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit dc4deb40aeefdf8b20f496626fe0ba28cbe248ed
yhoogstrate
parents: 32
diff changeset
338 <param name="input_format" value="bam"/>
5500eeb65605 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit dc4deb40aeefdf8b20f496626fe0ba28cbe248ed
yhoogstrate
parents: 32
diff changeset
339 <param name="index_source" value="history"/>
5500eeb65605 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit dc4deb40aeefdf8b20f496626fe0ba28cbe248ed
yhoogstrate
parents: 32
diff changeset
340 <param name="input" value="test_bam_01_input_a.sam" ftype="bam"/>
5500eeb65605 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit dc4deb40aeefdf8b20f496626fe0ba28cbe248ed
yhoogstrate
parents: 32
diff changeset
341 <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
5500eeb65605 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit dc4deb40aeefdf8b20f496626fe0ba28cbe248ed
yhoogstrate
parents: 32
diff changeset
342 <param name="include_fails" value="False"/>
5500eeb65605 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit dc4deb40aeefdf8b20f496626fe0ba28cbe248ed
yhoogstrate
parents: 32
diff changeset
343
5500eeb65605 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit dc4deb40aeefdf8b20f496626fe0ba28cbe248ed
yhoogstrate
parents: 32
diff changeset
344 <output name="output" file="test_bam_01_output_a.sam" compare="diff" lines_diff="4"/>
5500eeb65605 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit dc4deb40aeefdf8b20f496626fe0ba28cbe248ed
yhoogstrate
parents: 32
diff changeset
345 <output name="output_unmapped" file="test_bam_01_output_a.unmap.sam"/>
5500eeb65605 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit dc4deb40aeefdf8b20f496626fe0ba28cbe248ed
yhoogstrate
parents: 32
diff changeset
346 </test>
5500eeb65605 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit dc4deb40aeefdf8b20f496626fe0ba28cbe248ed
yhoogstrate
parents: 32
diff changeset
347
5500eeb65605 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit dc4deb40aeefdf8b20f496626fe0ba28cbe248ed
yhoogstrate
parents: 32
diff changeset
348 <test>
13
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
349 <param name="input_format" value="sam"/>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
350 <param name="index_source" value="history"/>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
351 <param name="input" value="test_bam_01_input_a.sam" ftype="sam"/>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
352 <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
353 <param name="include_fails" value="False"/>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
354
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
355 <output name="output" file="test_bam_01_output_a.sam" compare="diff" lines_diff="4"/>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
356 <output name="output_unmapped" file="test_bam_01_output_a.unmap.sam"/>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
357 </test>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
358
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
359 <!-- BED -->
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
360 <test>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
361 <param name="input_format" value="bed"/>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
362 <param name="index_source" value="history"/>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
363 <param name="input" value="test_bed_01_input_a.bed" ftype="bed"/>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
364 <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
365 <param name="include_fails" value="False"/>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
366
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
367 <output name="output" file="test_bed_01_output_a__only-matches.bed"/>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
368 </test>
1
f252cf28746d Uploaded
yhoogstrate
parents:
diff changeset
369 <test>
11
a5eb1023fc34 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 0acafcc4ce1261ec93eee1ad209a05246f4f02fd-dirty
yhoogstrate
parents: 9
diff changeset
370 <param name="input_format" value="bed"/>
a5eb1023fc34 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 0acafcc4ce1261ec93eee1ad209a05246f4f02fd-dirty
yhoogstrate
parents: 9
diff changeset
371 <param name="index_source" value="history"/>
a5eb1023fc34 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 0acafcc4ce1261ec93eee1ad209a05246f4f02fd-dirty
yhoogstrate
parents: 9
diff changeset
372 <param name="input" value="test_bed_01_input_a.bed" ftype="bed"/>
a5eb1023fc34 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 0acafcc4ce1261ec93eee1ad209a05246f4f02fd-dirty
yhoogstrate
parents: 9
diff changeset
373 <param name="input_chain" value="aToB.over.chain" ftype="txt"/>
13
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
374 <param name="include_fails" value="True"/>
11
a5eb1023fc34 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 0acafcc4ce1261ec93eee1ad209a05246f4f02fd-dirty
yhoogstrate
parents: 9
diff changeset
375
13
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
376 <output name="output" file="test_bed_01_output_a__all.bed"/>
1
f252cf28746d Uploaded
yhoogstrate
parents:
diff changeset
377 </test>
11
a5eb1023fc34 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 0acafcc4ce1261ec93eee1ad209a05246f4f02fd-dirty
yhoogstrate
parents: 9
diff changeset
378 <test>
a5eb1023fc34 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 0acafcc4ce1261ec93eee1ad209a05246f4f02fd-dirty
yhoogstrate
parents: 9
diff changeset
379 <param name="input_format" value="bed"/>
a5eb1023fc34 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 0acafcc4ce1261ec93eee1ad209a05246f4f02fd-dirty
yhoogstrate
parents: 9
diff changeset
380 <param name="index_source" value="history"/>
a5eb1023fc34 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 0acafcc4ce1261ec93eee1ad209a05246f4f02fd-dirty
yhoogstrate
parents: 9
diff changeset
381 <param name="input" value="test_bed_02_input_a.bed" ftype="bed"/>
a5eb1023fc34 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 0acafcc4ce1261ec93eee1ad209a05246f4f02fd-dirty
yhoogstrate
parents: 9
diff changeset
382 <param name="input_chain" value="aToB.over.chain" ftype="txt"/>
13
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
383 <param name="include_fails" value="False"/>
11
a5eb1023fc34 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 0acafcc4ce1261ec93eee1ad209a05246f4f02fd-dirty
yhoogstrate
parents: 9
diff changeset
384
a5eb1023fc34 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 0acafcc4ce1261ec93eee1ad209a05246f4f02fd-dirty
yhoogstrate
parents: 9
diff changeset
385 <output name="output" file="test_bed_02_output_a__only-matches.bed"/>
a5eb1023fc34 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 0acafcc4ce1261ec93eee1ad209a05246f4f02fd-dirty
yhoogstrate
parents: 9
diff changeset
386 </test>
a5eb1023fc34 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 0acafcc4ce1261ec93eee1ad209a05246f4f02fd-dirty
yhoogstrate
parents: 9
diff changeset
387 <test>
a5eb1023fc34 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 0acafcc4ce1261ec93eee1ad209a05246f4f02fd-dirty
yhoogstrate
parents: 9
diff changeset
388 <param name="input_format" value="bed"/>
a5eb1023fc34 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 0acafcc4ce1261ec93eee1ad209a05246f4f02fd-dirty
yhoogstrate
parents: 9
diff changeset
389 <param name="index_source" value="history"/>
a5eb1023fc34 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 0acafcc4ce1261ec93eee1ad209a05246f4f02fd-dirty
yhoogstrate
parents: 9
diff changeset
390 <param name="input" value="test_bed_02_input_a.bed" ftype="bed"/>
a5eb1023fc34 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 0acafcc4ce1261ec93eee1ad209a05246f4f02fd-dirty
yhoogstrate
parents: 9
diff changeset
391 <param name="input_chain" value="aToB.over.chain" ftype="txt"/>
13
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
392 <param name="include_fails" value="True"/>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
393
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
394 <output name="output" file="test_bed_02_output_a__all.bed"/>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
395 </test>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
396
18
d76352081273 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3d756e33e5a551c55cfb91fd95785ce102a8c41f-dirty
yhoogstrate
parents: 16
diff changeset
397 <!-- BigWig --><!-- Malfuncioning in CrossMap 0.2, but patched via galaxy toolshed installer -->
16
263581d4dd90 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 74570ff45544cfe08ef65d0b712f8d44da6f545c
yhoogstrate
parents: 13
diff changeset
398 <test>
263581d4dd90 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 74570ff45544cfe08ef65d0b712f8d44da6f545c
yhoogstrate
parents: 13
diff changeset
399 <param name="input_format" value="bigwig"/>
263581d4dd90 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 74570ff45544cfe08ef65d0b712f8d44da6f545c
yhoogstrate
parents: 13
diff changeset
400 <param name="index_source" value="history"/>
263581d4dd90 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 74570ff45544cfe08ef65d0b712f8d44da6f545c
yhoogstrate
parents: 13
diff changeset
401 <param name="input" value="test_bigwig_01_input_a.bw" ftype="bigwig"/>
263581d4dd90 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 74570ff45544cfe08ef65d0b712f8d44da6f545c
yhoogstrate
parents: 13
diff changeset
402 <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
263581d4dd90 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 74570ff45544cfe08ef65d0b712f8d44da6f545c
yhoogstrate
parents: 13
diff changeset
403 <param name="include_fails" value="False"/>
263581d4dd90 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 74570ff45544cfe08ef65d0b712f8d44da6f545c
yhoogstrate
parents: 13
diff changeset
404
263581d4dd90 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 74570ff45544cfe08ef65d0b712f8d44da6f545c
yhoogstrate
parents: 13
diff changeset
405 <output name="output" file="test_bigwig_01_output_a.bw"/>
263581d4dd90 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 74570ff45544cfe08ef65d0b712f8d44da6f545c
yhoogstrate
parents: 13
diff changeset
406 <output name="output2" file="test_bigwig_01_output_a.sorted.bgr"/>
18
d76352081273 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3d756e33e5a551c55cfb91fd95785ce102a8c41f-dirty
yhoogstrate
parents: 16
diff changeset
407 </test>
13
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
408 <!-- GFF -->
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
409 <test>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
410 <param name="input_format" value="gff"/>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
411 <param name="index_source" value="history"/>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
412 <param name="input" value="test_gff_01_input_a.gtf" ftype="gtf"/>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
413 <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
16
263581d4dd90 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 74570ff45544cfe08ef65d0b712f8d44da6f545c
yhoogstrate
parents: 13
diff changeset
414 <param name="include_fails" value="False"/>
13
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
415
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
416 <output name="output" file="test_gff_01_output_a__only-matches.gtf"/>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
417 </test>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
418 <test>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
419 <param name="input_format" value="gff"/>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
420 <param name="index_source" value="history"/>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
421 <param name="input" value="test_gff_01_input_a.gtf" ftype="gtf"/>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
422 <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
16
263581d4dd90 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 74570ff45544cfe08ef65d0b712f8d44da6f545c
yhoogstrate
parents: 13
diff changeset
423 <param name="include_fails" value="True"/>
11
a5eb1023fc34 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 0acafcc4ce1261ec93eee1ad209a05246f4f02fd-dirty
yhoogstrate
parents: 9
diff changeset
424
13
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
425 <output name="output" file="test_gff_01_output_a__all.gtf"/>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
426 </test>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
427
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
428 <!-- VCF -->
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
429 <test>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
430 <param name="input_format" value="vcf"/>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
431 <param name="index_source" value="history_all"/>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
432 <param name="input" value="test_vcf_01_input.vcf" ftype="vcf"/>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
433 <param name="input_chain" value="test_vcf_01.over.chain" ftype="csv"/>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
434 <param name="input_fasta" value="test_vcf_01.fasta" ftype="fasta"/>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
435 <param name="include_fails" value="False"/>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
436
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
437 <output name="output" file="test_vcf_01_output.vcf" compare="diff" lines_diff="4"/>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
438 <output name="output_unmapped" file="test_vcf_01_output.vcf.unmap"/>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
yhoogstrate
parents: 11
diff changeset
439 </test>
1
f252cf28746d Uploaded
yhoogstrate
parents:
diff changeset
440 </tests>
16
263581d4dd90 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 74570ff45544cfe08ef65d0b712f8d44da6f545c
yhoogstrate
parents: 13
diff changeset
441
263581d4dd90 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 74570ff45544cfe08ef65d0b712f8d44da6f545c
yhoogstrate
parents: 13
diff changeset
442 <!-- WIG - Doesn't understand fixedStep -->
263581d4dd90 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 74570ff45544cfe08ef65d0b712f8d44da6f545c
yhoogstrate
parents: 13
diff changeset
443 <test>
263581d4dd90 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 74570ff45544cfe08ef65d0b712f8d44da6f545c
yhoogstrate
parents: 13
diff changeset
444 <param name="input_format" value="wig"/>
263581d4dd90 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 74570ff45544cfe08ef65d0b712f8d44da6f545c
yhoogstrate
parents: 13
diff changeset
445 <param name="index_source" value="history"/>
263581d4dd90 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 74570ff45544cfe08ef65d0b712f8d44da6f545c
yhoogstrate
parents: 13
diff changeset
446 <param name="input" value="test_wig_01_input_a.wig" ftype="wig"/>
263581d4dd90 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 74570ff45544cfe08ef65d0b712f8d44da6f545c
yhoogstrate
parents: 13
diff changeset
447 <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
263581d4dd90 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 74570ff45544cfe08ef65d0b712f8d44da6f545c
yhoogstrate
parents: 13
diff changeset
448 <param name="include_fails" value="False"/>
263581d4dd90 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 74570ff45544cfe08ef65d0b712f8d44da6f545c
yhoogstrate
parents: 13
diff changeset
449
263581d4dd90 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 74570ff45544cfe08ef65d0b712f8d44da6f545c
yhoogstrate
parents: 13
diff changeset
450 <output name="output" file="test_wig_01_output_a.bw"/>
263581d4dd90 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 74570ff45544cfe08ef65d0b712f8d44da6f545c
yhoogstrate
parents: 13
diff changeset
451 <output name="output2" file="test_wig_01_output_a.sorted.bgr"/>
263581d4dd90 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 74570ff45544cfe08ef65d0b712f8d44da6f545c
yhoogstrate
parents: 13
diff changeset
452 </test>
1
f252cf28746d Uploaded
yhoogstrate
parents:
diff changeset
453 <help>
5
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a
yhoogstrate
parents: 1
diff changeset
454 CrossMap is versatile tool to convert genome coordinates or annotation files between genome
1
f252cf28746d Uploaded
yhoogstrate
parents:
diff changeset
455 assemblies. It supports mostly commonly used file types, including BAM, BED,BigWig, GFF,
f252cf28746d Uploaded
yhoogstrate
parents:
diff changeset
456 GTF, SAM, Wiggle, and VCF formats. For large plain text file types, such as BED, GFF, GTF
f252cf28746d Uploaded
yhoogstrate
parents:
diff changeset
457 and VCF, reading from remote servers and file compression are supported.
8
9750f8c1d3cb planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a-dirty
yhoogstrate
parents: 5
diff changeset
458
9750f8c1d3cb planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a-dirty
yhoogstrate
parents: 5
diff changeset
459 CrossMap bed
9750f8c1d3cb planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a-dirty
yhoogstrate
parents: 5
diff changeset
460 ------------
9750f8c1d3cb planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a-dirty
yhoogstrate
parents: 5
diff changeset
461 BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns.
9750f8c1d3cb planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a-dirty
yhoogstrate
parents: 5
diff changeset
462 BED format: http://genome.ucsc.edu/FAQ/FAQformat.html#format1
1
f252cf28746d Uploaded
yhoogstrate
parents:
diff changeset
463 </help>
f252cf28746d Uploaded
yhoogstrate
parents:
diff changeset
464
f252cf28746d Uploaded
yhoogstrate
parents:
diff changeset
465 <citations>
f252cf28746d Uploaded
yhoogstrate
parents:
diff changeset
466 <citation type="doi">10.1093/bioinformatics/btt730</citation>
f252cf28746d Uploaded
yhoogstrate
parents:
diff changeset
467 </citations>
f252cf28746d Uploaded
yhoogstrate
parents:
diff changeset
468 </tool>