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"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/transindel commit af32e767fd29667d3e29f1a202ad59d3dd498c84-dirty"
author jjohnson
date Mon, 30 Mar 2020 22:06:19 -0400
parents ba3910d7bd99
children
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ba3910d7bd99 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/transindel commit f102f45fafcda3ee868765784d2f69d2dcad6233-dirty"
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1 <macros>
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2 <token name="@VERSION@">1.0</token>
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3 <xml name="requirements">
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4 <requirements>
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5 <requirement type="package" version="@VERSION@">transindel</requirement>
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6 <yield/>
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7 </requirements>
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8 </xml>
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9 <xml name="citations">
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10 <citations>
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11 <citation type="doi">10.1186/s12864-018-4671-4</citation>
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12 <yield />
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13 </citations>
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14 </xml>
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15 <xml name="version_command">
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16 <version_command>transIndel_build_DNA.py -v</version_command>
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17 </xml>
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18 <xml name="reference_genome">
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19 <conditional name="rfasta">
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20 <param name="rfasta_source" type="select" label="Reference genome FASTA used for analyzing RNAseq data">
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21 <option value="cached" selected="true">Use a built-in genome fasta</option>
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22 <option value="history">Use a FASTA from history</option>
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23 </param>
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24 <when value="cached">
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25 <param name="ref_fa_builtin" type="select" label="Select a built-in FASTA" help="If your genome of interest is not listed, contact your Galaxy administrator">
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26 <options from_data_table="all_fasta">
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27 <filter type="sort_by" column="2" />
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28 <validator type="no_options" message="No FASTA is available for the selected input dataset" />
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29 </options>
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30 </param>
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31 </when>
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32 <when value="history">
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33 <param name="ref_fa_hist" type="data" format="fasta" label="Select a history FASTA" />
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34 </when>
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35 </conditional>
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36 </xml>
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37 <xml name="reference_gtf">
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38 <conditional name="rgtf">
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39 <param name="rgtf_source" type="select" label="Reference GTF annotation file used for analyzing RNAseq data">
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40 <option value="cached" selected="true">Use a built-in transcriptome</option>
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41 <option value="history">Use a GTF from history</option>
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42 </param>
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43 <when value="cached">
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44 <param name="ref_gtf_builtin" type="select" label="Select a built-in GTF" help="If the GTF file for your transcriptome of interest is not listed, contact your Galaxy administrator">
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45 <options from_data_table="gene_sets">
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46 <filter type="sort_by" column="2" />
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47 <validator type="no_options" message="No GTF file is available." />
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48 </options>
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49 </param>
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50 </when>
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51 <when value="history">
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52 <param name="ref_gtf_hist" type="data" format="gtf" label="Select a history GTF" />
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53 </when>
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54 </conditional>
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55 </xml>
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56
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57 <xml name="build_opts" token_default_mapq_cutoff="60">
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58 <param argument="--mapq_cutoff" type="integer" value="@DEFAULT_MAPQ_CUTOFF@" label="minimal MapQ in SAM for support SV event"/>
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59 <param argument="--max_del_length" type="integer" value="1000000" label="maximum deletion length to be detected"/>
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60 </xml>
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61 <xml name="call_opts">
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62 <section name="call_opts" title="transIndel_call.py options" expanded="false">
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63 <param name="min_observation_count" argument="-c" type="integer" value="4" label="minimal observation count for Indel" help="(default 4)"/>
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64 <param name="min_depth" argument="-d" type="integer" value="10" label="minimal depth to call Indel" help="(default 10)"/>
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65 <param name="min_length" argument="-l" type="integer" value="10" label="minimal indel length to report" help="(default 10)"/>
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66 <param name="min_mapq" argument="-m" type="integer" value="15" label="minimal mapq of read from BAM file to call indel" help="(default 15)"/>
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67 <param name="min_allele_frequency" argument="-f" type="float" value="0.1" min="0" max="1.0" label="minimal variant allele frequency" help="(default 0.1)"/>
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68 <conditional name="regions">
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69 <param name="regions_source" type="select" label="limit analysis to regions">
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70 <option value="none">No limit</option>
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71 <option value="text">text entry</option>
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72 <option value="bed">BED file</option>
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73 </param>
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74 <when value="none"/>
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75 <when value="text">
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76 <param name="target" argument="-t" type="text" value="" label="samtools region string">
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77 </param>
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78 </when>
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79 <when value="bed">
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80 <param name="target" argument="-t" type="data" format="bed" label="BED file of regions to report"/>
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81 </when>
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82 </conditional>
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83 </section>
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84 </xml>
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85 <xml name="transindel_call">
ba3910d7bd99 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/transindel commit f102f45fafcda3ee868765784d2f69d2dcad6233-dirty"
jjohnson
parents:
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86 <conditional name="transIndel_call">
ba3910d7bd99 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/transindel commit f102f45fafcda3ee868765784d2f69d2dcad6233-dirty"
jjohnson
parents:
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87 <param name="run_transIndel_call" type="select" label="Produce a VCF file using transIndel_call.py">
ba3910d7bd99 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/transindel commit f102f45fafcda3ee868765784d2f69d2dcad6233-dirty"
jjohnson
parents:
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88 <option value="yes">Yes</option>
ba3910d7bd99 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/transindel commit f102f45fafcda3ee868765784d2f69d2dcad6233-dirty"
jjohnson
parents:
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89 <option value="no">No</option>
ba3910d7bd99 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/transindel commit f102f45fafcda3ee868765784d2f69d2dcad6233-dirty"
jjohnson
parents:
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90 </param>
ba3910d7bd99 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/transindel commit f102f45fafcda3ee868765784d2f69d2dcad6233-dirty"
jjohnson
parents:
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91 <when value="yes">
ba3910d7bd99 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/transindel commit f102f45fafcda3ee868765784d2f69d2dcad6233-dirty"
jjohnson
parents:
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92 <yield/>
ba3910d7bd99 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/transindel commit f102f45fafcda3ee868765784d2f69d2dcad6233-dirty"
jjohnson
parents:
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93 <expand macro="call_opts"/>
ba3910d7bd99 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/transindel commit f102f45fafcda3ee868765784d2f69d2dcad6233-dirty"
jjohnson
parents:
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94 </when>
ba3910d7bd99 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/transindel commit f102f45fafcda3ee868765784d2f69d2dcad6233-dirty"
jjohnson
parents:
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95 <when value="no"/>
ba3910d7bd99 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/transindel commit f102f45fafcda3ee868765784d2f69d2dcad6233-dirty"
jjohnson
parents:
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96 </conditional>
ba3910d7bd99 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/transindel commit f102f45fafcda3ee868765784d2f69d2dcad6233-dirty"
jjohnson
parents:
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97 </xml>
ba3910d7bd99 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/transindel commit f102f45fafcda3ee868765784d2f69d2dcad6233-dirty"
jjohnson
parents:
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98 </macros>