crossmap: crossmap.xml annotate

annotate crossmap.xml @ 24:b586c38fc381 draft

planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 290b453ad2abdb65322ec2e50889aaf2b03bb095-dirty

author	yhoogstrate
date	Fri, 28 Aug 2015 09:35:52 -0400
parents	b55865ba56c8
children	a366e3148677

rev	line source
24 b586c38fc381 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 290b453ad2abdb65322ec2e50889aaf2b03bb095-dirty yhoogstrate parents: 23 diff changeset	1 <tool id="crossmap" name="CrossMap" version="0.2.b">
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>
20 386e76dfcd77 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb-dirty yhoogstrate parents: 18 diff changeset	5 <requirement type="package" version="0.1">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
263581d4dd90 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 74570ff45544cfe08ef65d0b712f8d44da6f545c yhoogstrate parents: 13 diff changeset	15 <version_command>CrossMap.py 2>&1 \| head -n 1 \| grep -E --only-matching 'CrossMap.*'</version_command>
263581d4dd90 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 74570ff45544cfe08ef65d0b712f8d44da6f545c yhoogstrate parents: 13 diff changeset	16
1 f252cf28746d Uploaded yhoogstrate parents: diff changeset	17 <command>
5 39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	18 CrossMap.py
13 7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	19 ${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	20
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	21 #if $multiple.input_format == "vcf" and $multiple.seq_source.index_source == "cached"
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	22 <!-- This is the 2nd dbkey, and the corresponding value has to be looked up -->
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	23 "${filter(lambda x: str( x[1] ) == str($multiple.seq_source.input_chain ), $__app__.tool_data_tables['liftOver'].get_fields())[0][2] }"
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	24 #else
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	25 "$multiple.seq_source.input_chain"
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	26 #end if
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	27
13 7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	28 #if $multiple.input_format in ["bam", "sam"]
5 39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	29 -m $multiple.insert_size
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	30 -s $multiple.insert_size_stdev
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	31 -t $multiple.insert_size_fold
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	32 #end if
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	33
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	34 "$multiple.seq_source.input"
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	35
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	36 #if $multiple.input_format == "vcf"
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	37 "$multiple.seq_source.input_fasta"
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	38 #end if
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	39
13 7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	40 #if str($multiple.include_fails) == "True"
11 a5eb1023fc34 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 0acafcc4ce1261ec93eee1ad209a05246f4f02fd-dirty yhoogstrate parents: 9 diff changeset	41 >
a5eb1023fc34 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 0acafcc4ce1261ec93eee1ad209a05246f4f02fd-dirty yhoogstrate parents: 9 diff changeset	42 #end if
9 0cae6e3273a8 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 0acafcc4ce1261ec93eee1ad209a05246f4f02fd yhoogstrate parents: 8 diff changeset	43
11 a5eb1023fc34 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 0acafcc4ce1261ec93eee1ad209a05246f4f02fd-dirty yhoogstrate parents: 9 diff changeset	44 "$output"
13 7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	45
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	46 #if $multiple.input_format in ["bam", "sam"]
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	47 ; mv "${output}.${multiple.input_format}" "$output"
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	48 ; mv "${output}.unmap.${multiple.input_format}" "$output_unmapped"
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	49 #else if $multiple.input_format in ["vcf"]
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	50 ; mv "${output}" "$output"
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	51 ; mv "${output}.unmap" "$output_unmapped"
16 263581d4dd90 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 74570ff45544cfe08ef65d0b712f8d44da6f545c yhoogstrate parents: 13 diff changeset	52 #else if $multiple.input_format in ["wig", "bigwig"]
263581d4dd90 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 74570ff45544cfe08ef65d0b712f8d44da6f545c yhoogstrate parents: 13 diff changeset	53 ; mv "${output}.bw" "$output"
263581d4dd90 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 74570ff45544cfe08ef65d0b712f8d44da6f545c yhoogstrate parents: 13 diff changeset	54 ; mv "${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	55 #end if
1 f252cf28746d Uploaded yhoogstrate parents: diff changeset	56 </command>
f252cf28746d Uploaded yhoogstrate parents: diff changeset	57
f252cf28746d Uploaded yhoogstrate parents: diff changeset	58 <inputs>
f252cf28746d Uploaded yhoogstrate parents: diff changeset	59 <conditional name="multiple">
5 39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	60 <param name="input_format" type="select" label="Convert a file of the following format">
13 7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	61 <option value="bam">BAM</option>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	62 <option value="sam">SAM</option>
5 39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	63 <option value="bed">BED or BED-like</option>
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	64 <option value="bigwig">BigWig</option>
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	65 <option value="gff">GFF or GTF</option>
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	66 <option value="vcf">VCF</option>
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	67 <option value="wig">Wiggle or bedGraph</option>
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	68 </param>
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	69 <when value="bam">
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	70 <conditional name="seq_source">
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	71 <param name="index_source" type="select" label="Source for LiftOver Data (chain file)">
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	72 <option value="cached">Local data (in galaxy)</option>
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	73 <option value="history">From History</option>
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	74 </param>
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	75 <when value="cached">
13 7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	76 <param type="data" format="bam" name="input" label="BAM/SAM file">
5 39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	77 <validator type="unspecified_build" />
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	78 <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." />
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	79 </param>
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	80 <param name="input_chain" type="select" label="Lift Over To">
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	81 <options from_file="liftOver.loc">
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	82 <column name="name" index="1"/>
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	83 <column name="value" index="2"/>
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	84 <column name="dbkey" index="0"/>
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	85 <filter type="data_meta" ref="input" key="dbkey" column="0" />
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	86 </options>
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	87 </param>
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	88 </when>
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	89 <when value="history">
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	90 <param type="data" format="bam,sam" name="input" label="BAM/SAM file" />
11 a5eb1023fc34 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 0acafcc4ce1261ec93eee1ad209a05246f4f02fd-dirty yhoogstrate parents: 9 diff changeset	91 <param type="data" format="csv" name="input_chain" label="LiftOver chain file" />
5 39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	92 </when>
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	93 </conditional>
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	94
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	95 <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]" />
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	96 <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]" />
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	97 <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]" />
13 7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	98
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	99 <param name="include_fails" type="hidden" tvalue="False" />
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	100 </when>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	101 <when value="sam"><!-- BAM and SAM are exactly the same conditions, but they need to be separate to get the proper output format -->
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	102 <conditional name="seq_source">
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	103 <param name="index_source" type="select" label="Source for LiftOver Data (chain file)">
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	104 <option value="cached">Local data (in galaxy)</option>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	105 <option value="history">From History</option>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	106 </param>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	107 <when value="cached">
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	108 <param type="data" format="sam" name="input" label="BAM/SAM file">
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	109 <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	110 <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	111 </param>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	112 <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	113 <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	114 <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	115 <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	116 <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	117 <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	118 </options>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	119 </param>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	120 </when>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	121 <when value="history">
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	122 <param type="data" format="bam,sam" name="input" label="BAM/SAM file" />
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	123 <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	124 </when>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	125 </conditional>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	126
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	127 <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]" />
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	128 <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]" />
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	129 <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]" />
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	130
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	131 <param name="include_fails" type="hidden" tvalue="False" />
5 39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	132 </when>
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	133 <when value="bed">
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	134 <conditional name="seq_source">
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	135 <param name="index_source" type="select" label="Source for LiftOver Data (chain file)">
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	136 <option value="cached">Local data (in galaxy)</option>
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	137 <option value="history">From History</option>
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	138 </param>
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	139 <when value="cached">
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	140 <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.">
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	141 <validator type="unspecified_build" />
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	142 <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." />
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	143 </param>
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	144 <param name="input_chain" type="select" label="Lift Over To">
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	145 <options from_file="liftOver.loc">
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	146 <column name="name" index="1"/>
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	147 <column name="value" index="2"/>
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	148 <column name="dbkey" index="0"/>
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	149 <filter type="data_meta" ref="input" key="dbkey" column="0" />
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	150 </options>
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	151 </param>
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	152 </when>
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	153 <when value="history">
9 0cae6e3273a8 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 0acafcc4ce1261ec93eee1ad209a05246f4f02fd yhoogstrate parents: 8 diff changeset	154 <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." />
11 a5eb1023fc34 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 0acafcc4ce1261ec93eee1ad209a05246f4f02fd-dirty yhoogstrate parents: 9 diff changeset	155 <param type="data" format="csv" name="input_chain" label="LiftOver chain file" />
5 39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	156 </when>
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	157 </conditional>
13 7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	158
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	159 <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')" />
5 39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	160 </when>
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	161 <when value="bigwig">
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	162 <conditional name="seq_source">
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	163 <param name="index_source" type="select" label="Source for LiftOver Data (chain file)">
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	164 <option value="cached">Local data (in galaxy)</option>
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	165 <option value="history">From History</option>
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	166 </param>
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	167 <when value="cached">
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	168 <param format="bigwig" name="input" type="data" label="BigWig file">
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	169 <validator type="unspecified_build" />
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	170 <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." />
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	171 </param>
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	172 <param name="input_chain" type="select" label="Lift Over To">
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	173 <options from_file="liftOver.loc">
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	174 <column name="name" index="1"/>
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	175 <column name="value" index="2"/>
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	176 <column name="dbkey" index="0"/>
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	177 <filter type="data_meta" ref="input" key="dbkey" column="0" />
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	178 </options>
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	179 </param>
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	180 </when>
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	181 <when value="history">
11 a5eb1023fc34 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 0acafcc4ce1261ec93eee1ad209a05246f4f02fd-dirty yhoogstrate parents: 9 diff changeset	182 <param type="data" format="bigwig" name="input" label="BigWig file" />
a5eb1023fc34 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 0acafcc4ce1261ec93eee1ad209a05246f4f02fd-dirty yhoogstrate parents: 9 diff changeset	183 <param type="data" format="csv" name="input_chain" label="LiftOver chain file" />
5 39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	184 </when>
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	185 </conditional>
16 263581d4dd90 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 74570ff45544cfe08ef65d0b712f8d44da6f545c yhoogstrate parents: 13 diff changeset	186
263581d4dd90 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 74570ff45544cfe08ef65d0b712f8d44da6f545c yhoogstrate parents: 13 diff changeset	187 <param name="include_fails" type="hidden" tvalue="False" />
5 39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	188 </when>
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	189 <when value="gff">
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	190 <conditional name="seq_source">
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	191 <param name="index_source" type="select" label="Source for LiftOver Data (chain file)">
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	192 <option value="cached">Local data (in galaxy)</option>
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	193 <option value="history">From History</option>
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	194 </param>
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	195 <when value="cached">
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	196 <param format="gtf,gff,gff3" name="input" type="data" label="GTF/GFF file">
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	197 <validator type="unspecified_build" />
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	198 <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." />
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	199 </param>
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	200 <param name="input_chain" type="select" label="Lift Over To">
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	201 <options from_file="liftOver.loc">
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	202 <column name="name" index="1"/>
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	203 <column name="value" index="2"/>
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	204 <column name="dbkey" index="0"/>
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	205 <filter type="data_meta" ref="input" key="dbkey" column="0" />
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	206 </options>
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	207 </param>
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	208 </when>
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	209 <when value="history">
11 a5eb1023fc34 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 0acafcc4ce1261ec93eee1ad209a05246f4f02fd-dirty yhoogstrate parents: 9 diff changeset	210 <param type="data" format="gtf,gff,gff3" name="input" label="GTF/GFF file" />
a5eb1023fc34 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 0acafcc4ce1261ec93eee1ad209a05246f4f02fd-dirty yhoogstrate parents: 9 diff changeset	211 <param type="data" format="csv" name="input_chain" label="LiftOver chain file" />
5 39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	212 </when>
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	213 </conditional>
13 7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	214
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	215 <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')" />
5 39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	216 </when>
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	217 <when value="vcf">
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	218 <conditional name="seq_source">
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	219 <param name="index_source" type="select" label="Source for LiftOver Data">
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	220 <option value="cached">Local data (in galaxy)</option>
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	221 <option value="history_chain">Chain file from History</option>
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	222 <option value="history_all">Chain & FASTA files from History</option>
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	223 </param>
13 7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	224
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	225 <when value="cached">
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	226 <param type="data" format="vcf" name="input" label="VCF file">
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	227 <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	228 <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	229 </param>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	230
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	231 <!-- automatically fetch a FASTA file from the same DBKEY as the chain file -->
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	232 <param name="input_chain" type="select" label="Lift Over To (Chain file)">
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	233 <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	234 <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	235 <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 -->
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	236 <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	237 <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	238 </options>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	239 </param>
5 39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	240
13 7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	241 <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">
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	242 <options from_file="all_fasta.loc">
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	243 <column name="name" index="2"/>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	244 <column name="value" index="3"/>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	245 <column name="dbkey" index="1"/>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	246 <filter type="param_value" ref="input_chain" column="1" />
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	247 </options>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	248 </param>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	249 </when>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	250
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	251 <when value="history_chain">
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	252 <param type="data" format="vcf" name="input" label="VCF file">
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	253 <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	254 <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." />
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	255 </param>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	256 <param type="data" format="csv" name="input_chain" multiple="false" 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	257 <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">
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	258 <options from_file="all_fasta.loc">
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	259 <column name="name" index="2"/>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	260 <column name="value" index="3"/>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	261 <column name="dbkey" index="1"/>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	262 </options>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	263 </param>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	264 </when>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	265
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	266 <when value="history_all">
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	267 <param type="data" format="vcf" name="input" label="VCF file" />
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	268 <param type="data" format="csv" name="input_chain" multiple="false" 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	269 <param type="data" format="fasta" name="input_fasta" multiple="false" label="Full genome FASTA file" />
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	270 </when>
5 39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	271 </conditional>
13 7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	272
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	273 <param name="include_fails" type="hidden" tvalue="False" />
5 39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	274 </when>
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	275 <when value="wig">
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	276 <conditional name="seq_source">
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	277 <param name="index_source" type="select" label="Source for LiftOver Data (chain file)">
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	278 <option value="cached">Local data (in galaxy)</option>
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	279 <option value="history">From History</option>
39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	280 </param>
13 7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	281 <when value="cached">
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	282 <param format="wig" name="input" type="data" label="Wiggle file">
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	283 <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	284 <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	285 </param>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	286 <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	287 <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	288 <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	289 <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	290 <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	291 <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	292 </options>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	293 </param>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	294 </when>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	295 <when value="history">
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	296 <param format="wig" name="input" type="data" label="Wiggle file" />
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	297 <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	298 </when>
5 39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	299 </conditional>
16 263581d4dd90 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 74570ff45544cfe08ef65d0b712f8d44da6f545c yhoogstrate parents: 13 diff changeset	300
263581d4dd90 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 74570ff45544cfe08ef65d0b712f8d44da6f545c yhoogstrate parents: 13 diff changeset	301 <param name="include_fails" type="hidden" tvalue="False" />
5 39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	302 </when>
1 f252cf28746d Uploaded yhoogstrate parents: diff changeset	303 </conditional>
f252cf28746d Uploaded yhoogstrate parents: diff changeset	304 </inputs>
f252cf28746d Uploaded yhoogstrate parents: diff changeset	305
f252cf28746d Uploaded yhoogstrate parents: diff changeset	306 <outputs>
13 7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	307 <data format="text" name="output" label="${tool.name} on ">
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	308 <change_format>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	309 <when input="multiple.input_format" value="bam" format="bam" />
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	310 <when input="multiple.input_format" value="sam" format="sam" />
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	311 <when input="multiple.input_format" value="bed" format="bed" />
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	312 <when input="multiple.input_format" value="bigwig" format="bigwig" />
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	313 <when input="multiple.input_format" value="gff" format="gff" />
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	314 <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	315 <when input="imultiple.nput_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	316 </change_format>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	317 </data>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	318
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	319 <data format="text" name="output_unmapped" label="${tool.name} unmapped on ">
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	320 <filter>input_format in ["bam" , "vcf"]</filter>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	321 <change_format>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	322 <when input="multiple.input_format" value="bam" format="bam" />
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	323 <when input="multiple.input_format" value="vcf" format="vcf" />
16 263581d4dd90 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 74570ff45544cfe08ef65d0b712f8d44da6f545c yhoogstrate parents: 13 diff changeset	324 </change_format>
263581d4dd90 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 74570ff45544cfe08ef65d0b712f8d44da6f545c yhoogstrate parents: 13 diff changeset	325 </data>
263581d4dd90 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 74570ff45544cfe08ef65d0b712f8d44da6f545c yhoogstrate parents: 13 diff changeset	326 <data format="text" name="output2" label="${tool.name} on ">
263581d4dd90 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 74570ff45544cfe08ef65d0b712f8d44da6f545c yhoogstrate parents: 13 diff changeset	327 <filter>input_format in ["wig"]</filter>
263581d4dd90 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 74570ff45544cfe08ef65d0b712f8d44da6f545c yhoogstrate parents: 13 diff changeset	328 <change_format>
263581d4dd90 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 74570ff45544cfe08ef65d0b712f8d44da6f545c yhoogstrate parents: 13 diff changeset	329 <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	330 </change_format>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	331 </data>
1 f252cf28746d Uploaded yhoogstrate parents: diff changeset	332 </outputs>
f252cf28746d Uploaded yhoogstrate parents: diff changeset	333
f252cf28746d Uploaded yhoogstrate parents: diff changeset	334 <tests>
13 7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	335 <!-- BAM/SAM -->
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	336 <test>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	337 <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	338 <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	339 <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	340 <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	341 <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	342
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	343 <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	344 <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	345 </test>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	346
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	347 <!-- BED -->
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	348 <test>
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="bed"/>
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_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	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_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	356 </test>
1 f252cf28746d Uploaded yhoogstrate parents: diff changeset	357 <test>
11 a5eb1023fc34 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 0acafcc4ce1261ec93eee1ad209a05246f4f02fd-dirty yhoogstrate parents: 9 diff changeset	358 <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	359 <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	360 <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	361 <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	362 <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	363
13 7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	364 <output name="output" file="test_bed_01_output_a__all.bed"/>
1 f252cf28746d Uploaded yhoogstrate parents: diff changeset	365 </test>
11 a5eb1023fc34 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 0acafcc4ce1261ec93eee1ad209a05246f4f02fd-dirty yhoogstrate parents: 9 diff changeset	366 <test>
a5eb1023fc34 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 0acafcc4ce1261ec93eee1ad209a05246f4f02fd-dirty yhoogstrate parents: 9 diff changeset	367 <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	368 <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	369 <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	370 <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	371 <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	372
a5eb1023fc34 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 0acafcc4ce1261ec93eee1ad209a05246f4f02fd-dirty yhoogstrate parents: 9 diff changeset	373 <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	374 </test>
a5eb1023fc34 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 0acafcc4ce1261ec93eee1ad209a05246f4f02fd-dirty yhoogstrate parents: 9 diff changeset	375 <test>
a5eb1023fc34 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 0acafcc4ce1261ec93eee1ad209a05246f4f02fd-dirty yhoogstrate parents: 9 diff changeset	376 <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	377 <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	378 <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	379 <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	380 <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	381
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	382 <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	383 </test>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	384
18 d76352081273 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3d756e33e5a551c55cfb91fd95785ce102a8c41f-dirty yhoogstrate parents: 16 diff changeset	385 <!-- 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	386 <test>
263581d4dd90 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 74570ff45544cfe08ef65d0b712f8d44da6f545c yhoogstrate parents: 13 diff changeset	387 <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	388 <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	389 <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	390 <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	391 <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	392
263581d4dd90 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 74570ff45544cfe08ef65d0b712f8d44da6f545c yhoogstrate parents: 13 diff changeset	393 <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	394 <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	395 </test>
13 7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	396 <!-- GFF -->
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	397 <test>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	398 <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	399 <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	400 <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	401 <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	402 <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	403
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	404 <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	405 </test>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	406 <test>
7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	407 <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	408 <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	409 <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	410 <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	411 <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	412
13 7e32d2a88c07 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty yhoogstrate parents: 11 diff changeset	413 <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	414 </test>
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 <!-- VCF -->
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 <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	419 <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	420 <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	421 <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	422 <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	423 <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	424
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_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	426 <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	427 </test>
1 f252cf28746d Uploaded yhoogstrate parents: diff changeset	428 </tests>
16 263581d4dd90 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 74570ff45544cfe08ef65d0b712f8d44da6f545c yhoogstrate parents: 13 diff changeset	429
263581d4dd90 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 74570ff45544cfe08ef65d0b712f8d44da6f545c yhoogstrate parents: 13 diff changeset	430 <!-- 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	431 <test>
263581d4dd90 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 74570ff45544cfe08ef65d0b712f8d44da6f545c yhoogstrate parents: 13 diff changeset	432 <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	433 <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	434 <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	435 <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	436 <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	437
263581d4dd90 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 74570ff45544cfe08ef65d0b712f8d44da6f545c yhoogstrate parents: 13 diff changeset	438 <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	439 <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	440 </test>
1 f252cf28746d Uploaded yhoogstrate parents: diff changeset	441 <help>
5 39d95e2675f5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a yhoogstrate parents: 1 diff changeset	442 CrossMap is versatile tool to convert genome coordinates or annotation files between genome
1 f252cf28746d Uploaded yhoogstrate parents: diff changeset	443 assemblies. It supports mostly commonly used file types, including BAM, BED,BigWig, GFF,
f252cf28746d Uploaded yhoogstrate parents: diff changeset	444 GTF, SAM, Wiggle, and VCF formats. For large plain text file types, such as BED, GFF, GTF
f252cf28746d Uploaded yhoogstrate parents: diff changeset	445 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	446
9750f8c1d3cb planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a-dirty yhoogstrate parents: 5 diff changeset	447 CrossMap bed
9750f8c1d3cb planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a-dirty yhoogstrate parents: 5 diff changeset	448 ------------
9750f8c1d3cb planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a-dirty yhoogstrate parents: 5 diff changeset	449 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	450 BED format: http://genome.ucsc.edu/FAQ/FAQformat.html#format1
1 f252cf28746d Uploaded yhoogstrate parents: diff changeset	451 </help>
f252cf28746d Uploaded yhoogstrate parents: diff changeset	452
f252cf28746d Uploaded yhoogstrate parents: diff changeset	453 <citations>
f252cf28746d Uploaded yhoogstrate parents: diff changeset	454 <citation type="doi">10.1093/bioinformatics/btt730</citation>
f252cf28746d Uploaded yhoogstrate parents: diff changeset	455 </citations>
f252cf28746d Uploaded yhoogstrate parents: diff changeset	456 </tool>

Mercurial > repos > yhoogstrate > crossmap

annotate crossmap.xml @ 24:b586c38fc381 draft