Mercurial > repos > mvdbeek > igv_take_screenshots

comparison igv_make_screenshots.xml @ 34:fbba13c34eb8 draft default tip

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"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit c6f25b122899a00695b5ca9e70d34e2c1d288236-dirty"
author mvdbeek
date Mon, 03 Feb 2020 09:40:58 +0000
parents 3f980046df62
children
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33:3f980046df62 34:fbba13c34eb8
1 <tool id="igv_make_screenshots" name="IGV_screenshots" version="0.1.2"> 1 <tool id="igv_make_screenshots" name="IGV_screenshots" version="0.1.3">
2 <macros> 2 <macros>
3 <token name="@DISPLAY_LINK@"><![CDATA[ 3 <token name="@DISPLAY_LINK@"><![CDATA[
4 #set $dataset_id = str($__app__.security.encode_id($inputsection.input.dataset.id)) 4 #set $dataset_id = str($__app__.security.encode_id($inputsection.input.dataset.id))
5 #set $user_id = str($__app__.security.encode_id($__user_id__)) 5 #set $user_id = str($__app__.security.encode_id($__user_id__))
6 #set $galaxy_url = $__app__.config.galaxy_infrastructure_url 6 #set $galaxy_url = $__app__.config.galaxy_infrastructure_url
25 <requirement type="package" version="2.0.94">libselinux-cos6-x86_64</requirement> 25 <requirement type="package" version="2.0.94">libselinux-cos6-x86_64</requirement>
26 <requirement type="package" version="1.0.2">openssl</requirement> 26 <requirement type="package" version="1.0.2">openssl</requirement>
27 <requirement type="package" version="1.9">samtools</requirement> 27 <requirement type="package" version="1.9">samtools</requirement>
28 <requirement type="package" version="8.30">coreutils</requirement> 28 <requirement type="package" version="8.30">coreutils</requirement>
29 --> 29 -->
30 <container type="docker">mvdbeek/igv_make_screenshots:0.1.2</container> 30 <container type="docker">mvdbeek/igv_make_screenshots:0.1.3</container>
31 </requirements> 31 </requirements>
32 <command detect_errors="exit_code"><![CDATA[ 32 <command detect_errors="exit_code"><![CDATA[
33 #if $genome_source.input_type_selector == 'history': 33 #if $genome_source.input_type_selector == 'history':
34 ln -s '$genome_source.genome' genome.fa && 34 ln -s '$genome_source.genome' genome.fa &&
35 #else: 35 #else:
49 cat '$load_session' > load_session.txt && 49 cat '$load_session' > load_session.txt &&
50 echo snapshotDirectory "\$PWD" >> load_session.txt && 50 echo snapshotDirectory "\$PWD" >> load_session.txt &&
51 cat load_session.txt '$script_file' '$exit_session' > igv_script.txt && 51 cat load_session.txt '$script_file' '$exit_session' > igv_script.txt &&
52 cp '$igv_session_remote' '$igv_session_out' 52 cp '$igv_session_remote' '$igv_session_out'
53 #if not $skip_screenshots: 53 #if not $skip_screenshots:
54 && xvfb-run --server-args="-screen 0 ${width}x${height}x24" igv -g genome.fa -o '$igv_preferences' --batch igv_script.txt && 54 && xvfb-run -a --server-args="-screen 0 ${width}x${height}x24" igv -g genome.fa -o '$igv_preferences' --batch igv_script.txt &&
55 mkdir screenshots && mv *.png screenshots || true 55 mkdir screenshots && mv *.png screenshots || touch screenshots/empty.png
56 #end if 56 #end if
57 ]]></command> 57 ]]></command>
58 <configfiles> 58 <configfiles>
59 <configfile name="igv_session"><![CDATA[<?xml version="1.0" encoding="UTF-8" standalone="no"?> 59 <configfile name="igv_session"><![CDATA[<?xml version="1.0" encoding="UTF-8" standalone="no"?>
60 <Session genome="genome.fa" hasGeneTrack="false" hasSequenceTrack="true" version="8"> 60 <Session genome="genome.fa" hasGeneTrack="false" hasSequenceTrack="true" version="8">