Mercurial > repos > iuc > jvarkit_wgscoverageplotter

annotate jvarkit_wgscoverageplotter.xml @ 0:859e0611960c draft

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"planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
author iuc
date Thu, 11 Feb 2021 08:00:58 +0000
parents
children ac048a34cac3
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859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
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1 <tool id="jvarkit_wgscoverageplotter" name="BAM Coverage Plotter" version="@TOOL_VERSION@+galaxy0">
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2 <description>Plot read coverage across a genomic contig</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">20201223</token>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="@TOOL_VERSION@">jvarkit-wgscoverageplotter</requirement>
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8 <requirement type="package" version="1.11">samtools</requirement>
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9 <requirement type="package" version="7.0.10_62">imagemagick</requirement>
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10 </requirements>
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11 <command detect_errors="exit_code"><![CDATA[
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12 #set include_regex = str($adv.include_contig_regex).strip()
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13 #set exclude_regex = str($adv.skip_contig_regex).strip()
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14 #set alignment_name = str($alignment_file.element_identifier)
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15 #if str($reference.source) == "history"
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16 ln -s '$reference.hist_genome' reference.fasta &&
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17 samtools faidx reference.fasta &&
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18 #else
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19 #set ref_path = str($reference.cached_genome.fields.path)
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20 #set ref_index_path = str($reference.cached_genome.fields.path) + '.fai'
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21 ln -s '$ref_path' reference.fasta &&
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22 ln -s '$ref_index_path' reference.fasta.fai &&
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23 #end if
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24 samtools view -H '$alignment_file' |grep -E '^(@HD|@SQ)' >reference.dict &&
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25 cat reference.dict &&
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26 ln -s '$alignment_file' '$alignment_name' &&
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27 ln -s '${alignment_file.metadata.bam_index}' '${alignment_name}.bai' &&
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28 wgscoverageplotter.sh
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29 --reference reference.fasta
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30 --dimension '$dimension'
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31 --output plot.svg
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32 $adv.disable_paired_overlap
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33 #if $include_regex
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34 -I '$include_regex'
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35 #end if
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36 #if $exclude_regex
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37 -X '$exclude_regex'
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38 #end if
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39 --mapq $adv.min_mapq
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40 --max-depth $adv.max_depth
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41 $adv.clip
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42 --min-contig-length '$adv.min_contig_length'
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43 --percentile $adv.percentile
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44 $adv.points
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45 #if str($adv.sample_filter.filter_by_sample) == "true"
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46 --samples '$adv.sample_filter.samples'
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47 --partition '$adv.sample_filter.partition'
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48 #end if
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49 '$alignment_name' &&
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50 #if str($format) == "SVG"
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51 mv plot.svg '$plot_output'
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52 #else
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53 convert plot.svg '$format:$plot_output'
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54 #end if
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55 ]]>
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56 </command>
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57 <inputs>
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58 <conditional name="reference">
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59 <param name="source" type="select"
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60 label="Will you select a reference genome from your history or use a built-in genome?">
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61 <option value="cached">Use a built-in genome</option>
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62 <option value="history" selected="true">Use a genome from my history</option>
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63 </param>
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64 <when value="cached">
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65 <!-- NOTE: wgscoverageplotter requires the genome to be both indexed (with samtools index)
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66 and also have a dictionary (from picard CreateSequenceDictionary). since there is no
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67 way to specify both of these requirements, we take the indexed genome and build a dictionary -->
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68 <param name="cached_genome" type="select"
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69 label="Reference genome"
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70 help="The FASTA reference genome that reads were mapped against.">
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71 <options from_data_table="fasta_indexes" />
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72 </param>
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73 </when>
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74 <when value="history">
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75 <param name="hist_genome" type="data" format="fasta"
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76 label="Reference genome"
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77 help="The FASTA reference genome that reads were mapped against."/>
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78 </when>
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79 </conditional>
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80 <param name="alignment_file" type="data" format="bam" label="BAM alignment" />
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81 <param argument="--dimension" value="1000x500" type="text" label="Image dimensions" />
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82 <param name="format" type="select" label="Output format" help="Note that SVG might not display correctly on all Galaxy servers">
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83 <option value="PNG" selected="true">PNG</option>
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84 <option value="SVG">SVG</option>
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85 </param>
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86 <section name="adv" title="Advanced options" expanded="false">
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87 <param argument="--disable-paired-overlap"
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88 name="disable_paired_overlap"
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89 type="boolean" truevalue="--disable-paired-overlap"
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90 falsevalue="" label="Count overlapping bases with mate for paired-end" />
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
91 <param argument="--include-contig-regex" name="include_contig_regex" type="text" label="Only keep chromosomes matching this regular expression." />
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
92 <param argument="--mapq" name="min_mapq" type="integer" value="1" label="Minimum mapping quality" />
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
93 <param argument="--max-depth"
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
94 name="max_depth"
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
95 type="integer"
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
96 label="y-axis (depth) limit of the plot"
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
97 value="-1"
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
98 help="The special value '-1' will first compute the average depth and the set the max depth to 2*average" />
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
99 <param argument="--clip"
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
100 type="boolean"
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
101 label="Clip the plot at the y-axis limit"
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
102 help="Default is to let the coverage plot exceed the y-axis limit"
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
103 truevalue="--clip"
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
104 falsevalue="" />
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
105 <param argument="--min-contig-length"
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
106 name="min_contig_length"
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
107 type="text"
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
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108 label="Skip chromosomes shorter than"
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
109 value="0"
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
110 help="A distance specified as a positive integer.">
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
111 <validator type="regex" message="A positive integer optionally followed by the suffixes b,bp,k,kb,m,mb is required">[0-9,]+(bp|b|kb|k|mb|m)?$</validator>
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
112 </param>
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
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113 <param argument="--percentile" type="select" label="How to bin the coverage under one pixel">
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
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114 <option value="median" selected="true">median</option>
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
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115 <option value="average">average</option>
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
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116 <option value="min">min</option>
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
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117 <option value="max">max</option>
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
118 </param>
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
119 <param argument="--points"
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
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120 type="boolean"
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
121 label="Plot coverage using points instead of areas"
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
122 truevalue="--points"
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
123 falsevalue=""
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
124 />
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
125 <param argument="--skip-contig-regex"
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
126 name="skip_contig_regex"
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
127 type="text"
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
128 label="Skip chromosomes matching this regular expression" />
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
129 <conditional name="sample_filter">
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
130 <param name="filter_by_sample" type="select" label="Filter by sample">
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
131 <option value="true">Yes</option>
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
132 <option value="false" selected="true">No</option>
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
133 </param>
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
134 <when value="true">
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
135 <param argument="--samples"
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
136 type="text"
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
137 label="Limit to these read groups"
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
138 help="See also --partition. Multiple read groups can be separated with commas.">
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
139 <validator type="expression" message="If a filter is being used, this field cannot be blank">len(str(value).strip()) > 0</validator>
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
140 </param>
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
141 <param argument="--partition" type="select" label="How to interpret identifiers in --samples" help="Partitions are modelled on the GATK logic as described here: https://gatk.broadinstitute.org/hc/en-us/articles/360051307491-DepthOfCoverage-BETA-#--partition-type">
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
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142 <option value="sample" selected="true">sample</option>
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
143 <option value="readgroup">readgroup</option>
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
144 <option value="library">library</option>
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
145 <option value="platform">platform</option>
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
146 <option value="sample_by_platform">sample_by_platform</option>
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
147 <option value="sample_by_platform_by_center">sample_by_platform_by_center</option>
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
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148 <option value="any">any</option>
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
149 </param>
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
150 </when>
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
151 <when value="false">
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
152 </when>
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
153 </conditional>
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
154 </section>
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
155 </inputs>
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
156 <outputs>
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
157 <data format="png" name="plot_output">
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
158 <change_format>
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
159 <when input="format" value="SVG" format="svg" />
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
160 </change_format>
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
161 </data>
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
162 </outputs>
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
163 <tests>
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
164 <test>
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
165 <conditional name="reference">
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iuc
parents:
diff changeset
166 <param name="source" value="history" />
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
167 <param name="hist_genome" ftype="fasta" value="reference.fasta" />
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
168 </conditional>
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
169 <param name="alignment_file" ftype="bam" value="sars_cov2_trimmed_cut.bam" />
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
170 <output name="plot_output">
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iuc
parents:
diff changeset
171 <assert_contents>
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iuc
parents:
diff changeset
172 <has_size value="26303" delta="15000" />
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
173 </assert_contents>
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iuc
parents:
diff changeset
174 </output>
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
175 </test>
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
176 <test>
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
177 <conditional name="reference">
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
178 <param name="source" value="history" />
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
179 <param name="hist_genome" ftype="fasta" value="reference.fasta" />
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
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180 </conditional>
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
181 <param name="alignment_file" ftype="bam" value="sars_cov2_trimmed_cut.bam" />
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
diff changeset
182 <param name="format" value="SVG" />
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
parents:
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183 <output name="plot_output">
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184 <assert_contents>
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
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185 <has_size value="7805" delta="2000"/>
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186 </assert_contents>
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
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187 </output>
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
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188 </test>
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
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189 <test>
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
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190 <conditional name="reference">
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
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191 <param name="source" value="history" />
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192 <param name="hist_genome" ftype="fasta" value="reference.fasta" />
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193 </conditional>
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
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194 <param name="alignment_file" ftype="bam" value="sars_cov2_trimmed_cut.bam" />
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195 <section name="adv">
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196 <param name="max_depth" value="50" />
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197 </section>
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
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198 <output name="plot_output">
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199 <assert_contents>
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
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200 <has_size value="25410" delta="15000" />
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
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201 </assert_contents>
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
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202 </output>
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
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203 </test>
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
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204 <test>
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
iuc
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205 <conditional name="reference">
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
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206 <param name="source" value="cached" />
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207 <param name="cached_genome" value="sars-cov-2-fragment" />
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208 </conditional>
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
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209 <param name="alignment_file" ftype="bam" value="sars_cov2_trimmed_cut.bam" />
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210 <output name="plot_output">
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211 <assert_contents>
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212 <has_size value="26303" delta="15000" />
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213 </assert_contents>
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214 </output>
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215 </test>
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216
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
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217 </tests>
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218 <help><![CDATA[
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219
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
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220 **WGSCoveragePlotter from the jvarkit toolkit**
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221
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
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222 WGSCoveragePlotter_ is a tool to plot the coverage of aligned reads across a genomic contig. It takes
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
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223 as input a BAM file and a genomic contig in FASTA format and produces an image in either PNG or SVG format
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
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224 showing the depth of read coverage across the contig.
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225
859e0611960c "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
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226 .. _WGSCoveragePlotter: http://lindenb.github.io/jvarkit/WGSCoveragePlotter.html
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227 ]]>
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228 </help>
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229 <citations>
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230 <citation type="doi">10.6084/m9.figshare.1425030</citation>
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231 </citations>
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232 </tool>