Mercurial > repos > yhoogstrate > crossmap

annotate crossmap.xml @ 0:bfcdabc062ca draft

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
author yhoogstrate
date Wed, 26 Aug 2015 11:04:47 -0400
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children e6efe37b456a
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0
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
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1 <tool id="crossmap" name="CrossMap" version="0.2.a">
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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2 <description>Convert genome coordinates or annotation files between genome assemblies</description>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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3
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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4 <requirements>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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5 <requirement type="package" version="312">ucsc_tools</requirement>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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6 <requirement type="package" version="0.2">crossmap</requirement>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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7 </requirements>
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bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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9 <stdio>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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10 <regex match="Usage: CrossMap.py" source="stdout" level="fatal"/>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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11 <regex match=".*" source="both" level="log"/>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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12 </stdio>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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14 <version_command>CrossMap.py 2&gt;&amp;1 | head -n 1 | grep -E --only-matching 'CrossMap.*'</version_command>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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16 <command>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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17 CrossMap.py
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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18 ${multiple.input_format.replace("sam","bam")}
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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20 #if $multiple.input_format == "vcf" and $multiple.seq_source.index_source == "cached"
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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21 <!-- This is the 2nd dbkey, and the corresponding value has to be looked up -->
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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22 "${filter(lambda x: str( x[1] ) == str($multiple.seq_source.input_chain ), $__app__.tool_data_tables['liftOver'].get_fields())[0][2] }"
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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23 #else
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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24 "$multiple.seq_source.input_chain"
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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25 #end if
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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26
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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27 #if $multiple.input_format in ["bam", "sam"]
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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28 -m $multiple.insert_size
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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29 -s $multiple.insert_size_stdev
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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30 -t $multiple.insert_size_fold
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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31 #end if
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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32
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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33 "$multiple.seq_source.input"
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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34
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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35 #if $multiple.input_format == "vcf"
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36 "$multiple.seq_source.input_fasta"
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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37 #end if
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38
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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39 #if str($multiple.include_fails) == "True"
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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40 >
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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41 #end if
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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42
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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43 "$output"
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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44
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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45 #if $multiple.input_format in ["bam", "sam"]
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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46 ; mv "${output}.${multiple.input_format}" "$output"
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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47 ; mv "${output}.unmap.${multiple.input_format}" "$output_unmapped"
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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48 #else if $multiple.input_format in ["vcf"]
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49 ; mv "${output}" "$output"
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50 ; mv "${output}.unmap" "$output_unmapped"
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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51 #else if $multiple.input_format in ["wig", "bigwig"]
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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52 ; mv "${output}.bw" "$output"
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53 ; mv "${output}.sorted.bgr" "$output2"
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54 #end if
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55 </command>
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56
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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57 <inputs>
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58 <conditional name="multiple">
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59 <param name="input_format" type="select" label="Convert a file of the following format">
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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60 <option value="bam">BAM</option>
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61 <option value="sam">SAM</option>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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62 <option value="bed">BED or BED-like</option>
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63 <option value="bigwig">BigWig</option>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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64 <option value="gff">GFF or GTF</option>
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65 <option value="vcf">VCF</option>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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66 <option value="wig">Wiggle or bedGraph</option>
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67 </param>
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68 <when value="bam">
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69 <conditional name="seq_source">
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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70 <param name="index_source" type="select" label="Source for LiftOver Data (chain file)">
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71 <option value="cached">Local data (in galaxy)</option>
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72 <option value="history">From History</option>
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73 </param>
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74 <when value="cached">
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75 <param type="data" format="bam" name="input" label="BAM/SAM file">
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76 <validator type="unspecified_build" />
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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77 <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." />
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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78 </param>
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79 <param name="input_chain" type="select" label="Lift Over To">
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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80 <options from_file="liftOver.loc">
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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81 <column name="name" index="1"/>
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82 <column name="value" index="2"/>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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83 <column name="dbkey" index="0"/>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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84 <filter type="data_meta" ref="input" key="dbkey" column="0" />
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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85 </options>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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86 </param>
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87 </when>
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88 <when value="history">
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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89 <param type="data" format="bam,sam" name="input" label="BAM/SAM file" />
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90 <param type="data" format="csv" name="input_chain" label="LiftOver chain file" />
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91 </when>
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92 </conditional>
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93
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94 <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]" />
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95 <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]" />
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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96 <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]" />
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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97
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98 <param name="include_fails" type="hidden" tvalue="False" />
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99 </when>
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100 <when value="sam"><!-- BAM and SAM are exactly the same conditions, but they need to be separate to get the proper output format -->
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101 <conditional name="seq_source">
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102 <param name="index_source" type="select" label="Source for LiftOver Data (chain file)">
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103 <option value="cached">Local data (in galaxy)</option>
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104 <option value="history">From History</option>
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105 </param>
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106 <when value="cached">
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107 <param type="data" format="sam" name="input" label="BAM/SAM file">
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108 <validator type="unspecified_build" />
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109 <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." />
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110 </param>
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111 <param name="input_chain" type="select" label="Lift Over To">
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112 <options from_file="liftOver.loc">
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113 <column name="name" index="1"/>
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114 <column name="value" index="2"/>
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115 <column name="dbkey" index="0"/>
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116 <filter type="data_meta" ref="input" key="dbkey" column="0" />
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117 </options>
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118 </param>
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119 </when>
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120 <when value="history">
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121 <param type="data" format="bam,sam" name="input" label="BAM/SAM file" />
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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122 <param type="data" format="csv" name="input_chain" label="LiftOver chain file" />
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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123 </when>
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124 </conditional>
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125
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126 <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]" />
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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127 <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]" />
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128 <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]" />
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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129
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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130 <param name="include_fails" type="hidden" tvalue="False" />
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131 </when>
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132 <when value="bed">
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133 <conditional name="seq_source">
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134 <param name="index_source" type="select" label="Source for LiftOver Data (chain file)">
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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135 <option value="cached">Local data (in galaxy)</option>
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136 <option value="history">From History</option>
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137 </param>
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138 <when value="cached">
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139 <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.">
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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140 <validator type="unspecified_build" />
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141 <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." />
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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142 </param>
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143 <param name="input_chain" type="select" label="Lift Over To">
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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144 <options from_file="liftOver.loc">
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145 <column name="name" index="1"/>
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146 <column name="value" index="2"/>
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147 <column name="dbkey" index="0"/>
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148 <filter type="data_meta" ref="input" key="dbkey" column="0" />
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149 </options>
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150 </param>
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151 </when>
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152 <when value="history">
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153 <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." />
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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154 <param type="data" format="csv" name="input_chain" label="LiftOver chain file" />
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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155 </when>
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156 </conditional>
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157
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158 <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')" />
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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159 </when>
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160 <when value="bigwig">
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161 <conditional name="seq_source">
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162 <param name="index_source" type="select" label="Source for LiftOver Data (chain file)">
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163 <option value="cached">Local data (in galaxy)</option>
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164 <option value="history">From History</option>
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165 </param>
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166 <when value="cached">
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167 <param format="bigwig" name="input" type="data" label="BigWig file">
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168 <validator type="unspecified_build" />
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169 <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." />
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170 </param>
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171 <param name="input_chain" type="select" label="Lift Over To">
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172 <options from_file="liftOver.loc">
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173 <column name="name" index="1"/>
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174 <column name="value" index="2"/>
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175 <column name="dbkey" index="0"/>
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176 <filter type="data_meta" ref="input" key="dbkey" column="0" />
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177 </options>
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178 </param>
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179 </when>
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180 <when value="history">
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181 <param type="data" format="bigwig" name="input" label="BigWig file" />
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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182 <param type="data" format="csv" name="input_chain" label="LiftOver chain file" />
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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183 </when>
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184 </conditional>
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185
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186 <param name="include_fails" type="hidden" tvalue="False" />
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187 </when>
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188 <when value="gff">
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189 <conditional name="seq_source">
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190 <param name="index_source" type="select" label="Source for LiftOver Data (chain file)">
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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191 <option value="cached">Local data (in galaxy)</option>
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192 <option value="history">From History</option>
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193 </param>
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194 <when value="cached">
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195 <param format="gtf,gff,gff3" name="input" type="data" label="GTF/GFF file">
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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196 <validator type="unspecified_build" />
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197 <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." />
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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198 </param>
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199 <param name="input_chain" type="select" label="Lift Over To">
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200 <options from_file="liftOver.loc">
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201 <column name="name" index="1"/>
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202 <column name="value" index="2"/>
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203 <column name="dbkey" index="0"/>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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204 <filter type="data_meta" ref="input" key="dbkey" column="0" />
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205 </options>
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206 </param>
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207 </when>
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208 <when value="history">
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209 <param type="data" format="gtf,gff,gff3" name="input" label="GTF/GFF file" />
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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210 <param type="data" format="csv" name="input_chain" label="LiftOver chain file" />
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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211 </when>
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212 </conditional>
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213
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214 <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')" />
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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215 </when>
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216 <when value="vcf">
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217 <conditional name="seq_source">
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218 <param name="index_source" type="select" label="Source for LiftOver Data">
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219 <option value="cached">Local data (in galaxy)</option>
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220 <option value="history_chain">Chain file from History</option>
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221 <option value="history_all">Chain &amp; FASTA files from History</option>
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222 </param>
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223
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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224 <when value="cached">
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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225 <param type="data" format="vcf" name="input" label="VCF file">
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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226 <validator type="unspecified_build" />
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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227 <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." />
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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228 </param>
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229
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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230 <!-- automatically fetch a FASTA file from the same DBKEY as the chain file -->
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231 <param name="input_chain" type="select" label="Lift Over To (Chain file)">
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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232 <options from_file="liftOver.loc">
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233 <column name="name" index="1" />
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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234 <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 -->
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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235 <column name="dbkey" index="0" />
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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236 <filter type="data_meta" ref="input" key="dbkey" column="0" />
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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237 </options>
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238 </param>
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239
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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240 <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">
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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241 <options from_file="all_fasta.loc">
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242 <column name="name" index="2"/>
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243 <column name="value" index="3"/>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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244 <column name="dbkey" index="1"/>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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245 <filter type="param_value" ref="input_chain" column="1" />
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246 </options>
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247 </param>
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248 </when>
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249
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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250 <when value="history_chain">
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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251 <param type="data" format="vcf" name="input" label="VCF file">
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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252 <validator type="unspecified_build" />
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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253 <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." />
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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254 </param>
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255 <param type="data" format="csv" name="input_chain" multiple="false" label="LiftOver chain file" />
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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256 <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">
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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257 <options from_file="all_fasta.loc">
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258 <column name="name" index="2"/>
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259 <column name="value" index="3"/>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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260 <column name="dbkey" index="1"/>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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261 </options>
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262 </param>
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263 </when>
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264
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265 <when value="history_all">
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266 <param type="data" format="vcf" name="input" label="VCF file" />
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267 <param type="data" format="csv" name="input_chain" multiple="false" label="LiftOver chain file" />
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268 <param type="data" format="fasta" name="input_fasta" multiple="false" label="Full genome FASTA file" />
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269 </when>
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270 </conditional>
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271
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272 <param name="include_fails" type="hidden" tvalue="False" />
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273 </when>
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274 <when value="wig">
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275 <conditional name="seq_source">
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276 <param name="index_source" type="select" label="Source for LiftOver Data (chain file)">
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277 <option value="cached">Local data (in galaxy)</option>
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278 <option value="history">From History</option>
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279 </param>
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280 <when value="cached">
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281 <param format="wig" name="input" type="data" label="Wiggle file">
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282 <validator type="unspecified_build" />
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283 <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." />
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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284 </param>
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285 <param name="input_chain" type="select" label="Lift Over To">
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286 <options from_file="liftOver.loc">
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287 <column name="name" index="1"/>
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288 <column name="value" index="2"/>
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289 <column name="dbkey" index="0"/>
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290 <filter type="data_meta" ref="input" key="dbkey" column="0" />
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291 </options>
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292 </param>
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293 </when>
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294 <when value="history">
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295 <param format="wig" name="input" type="data" label="Wiggle file" />
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296 <param type="data" format="csv" name="input_chain" label="LiftOver chain file" />
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297 </when>
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298 </conditional>
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299
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300 <param name="include_fails" type="hidden" tvalue="False" />
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301 </when>
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302 </conditional>
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303 </inputs>
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304
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305 <outputs>
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306 <data format="text" name="output" label="${tool.name} on ">
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307 <change_format>
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308 <when input="multiple.input_format" value="bam" format="bam" />
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309 <when input="multiple.input_format" value="sam" format="sam" />
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310 <when input="multiple.input_format" value="bed" format="bed" />
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311 <when input="multiple.input_format" value="bigwig" format="bigwig" />
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312 <when input="multiple.input_format" value="gff" format="gff" />
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313 <when input="multiple.input_format" value="vcf" format="vcf" />
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314 <when input="imultiple.nput_format" value="wig" format="bigwig" />
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315 </change_format>
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316 </data>
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317
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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318 <data format="text" name="output_unmapped" label="${tool.name} unmapped on ">
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319 <filter>input_format in ["bam" , "vcf"]</filter>
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320 <change_format>
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321 <when input="multiple.input_format" value="bam" format="bam" />
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322 <when input="multiple.input_format" value="vcf" format="vcf" />
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323 </change_format>
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324 </data>
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325 <data format="text" name="output2" label="${tool.name} on ">
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326 <filter>input_format in ["wig"]</filter>
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327 <change_format>
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328 <when input="multiple.input_format" value="wig" format="bedgraph" />
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329 </change_format>
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330 </data>
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331 </outputs>
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332
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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333 <tests>
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334 <!-- BAM/SAM -->
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335 <test>
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336 <param name="input_format" value="sam"/>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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337 <param name="index_source" value="history"/>
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338 <param name="input" value="test_bam_01_input_a.sam" ftype="sam"/>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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339 <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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340 <param name="include_fails" value="False"/>
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341
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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342 <output name="output" file="test_bam_01_output_a.sam" compare="diff" lines_diff="4"/>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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343 <output name="output_unmapped" file="test_bam_01_output_a.unmap.sam"/>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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344 </test>
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345
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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346 <!-- BED -->
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347 <test>
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348 <param name="input_format" value="bed"/>
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349 <param name="index_source" value="history"/>
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350 <param name="input" value="test_bed_01_input_a.bed" ftype="bed"/>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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351 <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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diff changeset
352 <param name="include_fails" value="False"/>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
353
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
354 <output name="output" file="test_bed_01_output_a__only-matches.bed"/>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
355 </test>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
356 <test>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
357 <param name="input_format" value="bed"/>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
358 <param name="index_source" value="history"/>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
359 <param name="input" value="test_bed_01_input_a.bed" ftype="bed"/>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
360 <param name="input_chain" value="aToB.over.chain" ftype="txt"/>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
361 <param name="include_fails" value="True"/>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
362
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
363 <output name="output" file="test_bed_01_output_a__all.bed"/>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
364 </test>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
365 <test>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
366 <param name="input_format" value="bed"/>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
367 <param name="index_source" value="history"/>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
368 <param name="input" value="test_bed_02_input_a.bed" ftype="bed"/>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
369 <param name="input_chain" value="aToB.over.chain" ftype="txt"/>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
370 <param name="include_fails" value="False"/>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
371
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
372 <output name="output" file="test_bed_02_output_a__only-matches.bed"/>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
373 </test>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
374 <test>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
375 <param name="input_format" value="bed"/>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
376 <param name="index_source" value="history"/>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
377 <param name="input" value="test_bed_02_input_a.bed" ftype="bed"/>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
378 <param name="input_chain" value="aToB.over.chain" ftype="txt"/>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
379 <param name="include_fails" value="True"/>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
380
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
381 <output name="output" file="test_bed_02_output_a__all.bed"/>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
382 </test>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
383
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
384 <!-- BigWig --><!-- Malfuncioning in CrossMap 0.2, but patched via galaxy toolshed installer -->
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
385 <test>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
386 <param name="input_format" value="bigwig"/>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
387 <param name="index_source" value="history"/>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
388 <param name="input" value="test_bigwig_01_input_a.bw" ftype="bigwig"/>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
389 <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
390 <param name="include_fails" value="False"/>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
391
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
392 <output name="output" file="test_bigwig_01_output_a.bw"/>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
393 <output name="output2" file="test_bigwig_01_output_a.sorted.bgr"/>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
394 </test>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
395 <!-- GFF -->
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
396 <test>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
397 <param name="input_format" value="gff"/>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
398 <param name="index_source" value="history"/>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
399 <param name="input" value="test_gff_01_input_a.gtf" ftype="gtf"/>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
400 <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
401 <param name="include_fails" value="False"/>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
402
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
403 <output name="output" file="test_gff_01_output_a__only-matches.gtf"/>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
404 </test>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
405 <test>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
406 <param name="input_format" value="gff"/>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
407 <param name="index_source" value="history"/>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
408 <param name="input" value="test_gff_01_input_a.gtf" ftype="gtf"/>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
409 <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
410 <param name="include_fails" value="True"/>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
411
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
412 <output name="output" file="test_gff_01_output_a__all.gtf"/>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
413 </test>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
414
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
415 <!-- VCF -->
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
416 <test>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
417 <param name="input_format" value="vcf"/>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
418 <param name="index_source" value="history_all"/>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
419 <param name="input" value="test_vcf_01_input.vcf" ftype="vcf"/>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
420 <param name="input_chain" value="test_vcf_01.over.chain" ftype="csv"/>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
421 <param name="input_fasta" value="test_vcf_01.fasta" ftype="fasta"/>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
422 <param name="include_fails" value="False"/>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
423
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
424 <output name="output" file="test_vcf_01_output.vcf" compare="diff" lines_diff="4"/>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
425 <output name="output_unmapped" file="test_vcf_01_output.vcf.unmap"/>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
426 </test>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
427 </tests>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
428
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
429 <!-- WIG - Doesn't understand fixedStep -->
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
430 <test>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
431 <param name="input_format" value="wig"/>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
432 <param name="index_source" value="history"/>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
433 <param name="input" value="test_wig_01_input_a.wig" ftype="wig"/>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
434 <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
435 <param name="include_fails" value="False"/>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
436
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
437 <output name="output" file="test_wig_01_output_a.bw"/>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
438 <output name="output2" file="test_wig_01_output_a.sorted.bgr"/>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
439 </test>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
diff changeset
440 <help>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
yhoogstrate
parents:
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441 CrossMap is versatile tool to convert genome coordinates or annotation files between genome
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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442 assemblies. It supports mostly commonly used file types, including BAM, BED,BigWig, GFF,
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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443 GTF, SAM, Wiggle, and VCF formats. For large plain text file types, such as BED, GFF, GTF
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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444 and VCF, reading from remote servers and file compression are supported.
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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445
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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446 CrossMap bed
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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447 ------------
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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448 BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns.
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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449 BED format: http://genome.ucsc.edu/FAQ/FAQformat.html#format1
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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450 </help>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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451
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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452 <citations>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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453 <citation type="doi">10.1093/bioinformatics/btt730</citation>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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454 </citations>
bfcdabc062ca planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit d4e9fe61901a612c78d9f26f172537b27fd2ddbb
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455 </tool>