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annotate star_fusion.xml @ 1:f2c3551338f2 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit d6a7537117d814677113ba9a8e4783a80dd228a2
author iuc
date Thu, 20 Apr 2017 08:12:02 -0400
parents 632b90370be0
children 6485791e9238
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f2c3551338f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit d6a7537117d814677113ba9a8e4783a80dd228a2
iuc
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1 <tool id="star_fusion" name="STAR-Fusion" version="0.5.4-3" profile="17.01">
0
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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2 <description>detect fusion genes in RNA-Seq data</description>
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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3 <requirements>
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4 <!-- Bio-conda -->
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5 <requirement type="package" version="0.5.4">star-fusion</requirement>
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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6 </requirements>
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7
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8 <stdio>
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9 <regex match="command not found" source="stderr" level="fatal"/>
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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10 <regex match="EXITING because of INPUT ERROR" source="stderr" level="fatal"/>
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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11 <regex match="FATAL ERROR" source="stderr" level="fatal"/>
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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12
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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13 <regex match="Warning:" source="stderr" level="warning"/>
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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14 <regex match="CMD:" source="stderr" level="warning"/>
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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16 <regex match="-done creating index file:" source="stderr" level="warning"/>
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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17 <regex match="-parsing GTF file:" source="stderr" level="warning"/>
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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18 <regex match="-building interval tree" source="stderr" level="warning"/>
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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19 <regex match="-parsing fusion evidence:" source="stderr" level="warning"/>
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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20 <regex match="-mapping reads to genes" source="stderr" level="warning"/>
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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21 <regex match="-outputting fusion candidates to file:" source="stderr" level="warning"/>
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23 <regex match="Process complete" source="stderr" level="warning"/>
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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24 </stdio>
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26 <version_command>STAR-Fusion --version 2>&amp;1 | grep version | grep -o -E "software version.*?"</version_command>
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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27
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28 <command><![CDATA[
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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29 ## 1. ensure the blastn file is provided as *.gz
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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30 if file --mime-type '${blast_pairs}' | grep -q /gzip\$; then
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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31 gzip_suffix='' ;
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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32 else
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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33 ## Older versions of gzip do not support the -k option to keep
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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34 ## the original file - this should be an universion solution
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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35
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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36 gzip -1 -c -- '${blast_pairs}' > '${blast_pairs}.gz' &&
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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37 gzip_suffix='.gz' ;
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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38 fi &&
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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39
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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40 ## 2. create reference index - using \$(pwd) is necessary, probably because the perl script changes work directory
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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41 ## - @todo once write a decent STAR and STAR Fusion data manager
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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42 prep_genome_lib.pl
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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43 --genome_fa '${fasta_type.ownFile}'
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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44 --gtf '${geneModel}'
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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45 --blast_pairs "${blast_pairs}\$gzip_suffix"
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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46 --CPU \${GALAXY_SLOTS:-1}
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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47 --output_dir "\$(pwd)/tmp_star_fusion_genome_dir"
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48 &&
1
f2c3551338f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit d6a7537117d814677113ba9a8e4783a80dd228a2
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49
f2c3551338f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit d6a7537117d814677113ba9a8e4783a80dd228a2
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50 ## Link in fastq files so they have appropriate extensions
f2c3551338f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit d6a7537117d814677113ba9a8e4783a80dd228a2
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51 #if str($input_params.input_source) != "use_chimeric":
f2c3551338f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit d6a7537117d814677113ba9a8e4783a80dd228a2
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52 #if $input_params.left_fq.is_of_type("fastq.gz"):
f2c3551338f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit d6a7537117d814677113ba9a8e4783a80dd228a2
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53 #set read1 = 'input_1.fastq.gz'
f2c3551338f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit d6a7537117d814677113ba9a8e4783a80dd228a2
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54 #else:
f2c3551338f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit d6a7537117d814677113ba9a8e4783a80dd228a2
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55 #set read1 = 'input_1.fastq'
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56 #end if
f2c3551338f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit d6a7537117d814677113ba9a8e4783a80dd228a2
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57 ln -f -s '${input_params.left_fq}' ${read1} &&
f2c3551338f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit d6a7537117d814677113ba9a8e4783a80dd228a2
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58
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59 #if $input_params.right_fq:
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60 #if $input_params.right_fq.is_of_type("fastq.gz"):
f2c3551338f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit d6a7537117d814677113ba9a8e4783a80dd228a2
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61 #set read2 = 'input_2.fastq.gz'
f2c3551338f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit d6a7537117d814677113ba9a8e4783a80dd228a2
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62 #else:
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63 #set read2 = 'input_2.fastq'
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64 #end if
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65 ln -f -s '${input_params.right_fq}' ${read2} &&
f2c3551338f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit d6a7537117d814677113ba9a8e4783a80dd228a2
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66 #end if
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67 #end if
0
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68
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69 ## 3. Run STAR-Fusion
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70 STAR-Fusion
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71 #if str($input_params.input_source) == "use_chimeric":
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72 --chimeric_junction '${input_params.chimeric_junction}'
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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73 #else:
1
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74 --left_fq ${read1}
0
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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75 #if $input_params.right_fq:
1
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76 --right_fq ${read2}
0
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77 #end if
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78 #end if
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79
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80 --genome_lib_dir "\$(pwd)/tmp_star_fusion_genome_dir"
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81
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82 #if str($params.settingsType) == "full":
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83 --min_junction_reads $params.min_junction_reads
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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84 --min_sum_frags $params.min_sum_frags
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85 --max_promiscuity $params.max_promiscuity
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86 --min_novel_junction_support $params.min_novel_junction_support
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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87 --min_alt_pct_junction $params.min_alt_pct_junction
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
88 --aggregate_novel_junction_dist $params.aggregate_novel_junction_dist
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
89 --E $params.E
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
90 #end if
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
91 ]]></command>
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
92
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
93 <inputs>
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
94 <conditional name="input_params">
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
95 <param name="input_source"
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
96 type="select"
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
97 label="Use output from earlier STAR run or let STAR Fusion control running STAR">
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
98 <option value="use_chimeric">Use output from earlier STAR</option>
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
99 <option value="use_fastq">Let STAR Fusion control running STAR</option>
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
100 </param>
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
101 <when value="use_chimeric">
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
102 <param name="chimeric_junction"
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
103 type="data"
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
104 format="interval"
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
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diff changeset
105 argument="--chimeric_junction"
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
106 label="Chimeric junction file from STAR (with STAR-Fusion settings)"/>
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
107 </when>
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
108 <when value="use_fastq">
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
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diff changeset
109 <param name="left_fq"
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
110 type="data"
1
f2c3551338f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit d6a7537117d814677113ba9a8e4783a80dd228a2
iuc
parents: 0
diff changeset
111 format="fastqsanger,fastqsanger.gz"
0
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
112 argument="--left_fq"
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
113 label="left.fq file"/>
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
114 <param name="right_fq"
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
115 type="data"
1
f2c3551338f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit d6a7537117d814677113ba9a8e4783a80dd228a2
iuc
parents: 0
diff changeset
116 format="fastqsanger,fastqsanger.gz"
0
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
117 optional="true"
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
118 argument="--right_fq"
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
119 label="right.fq file (actually optional, but highly recommended)"/>
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
120 </when>
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
121 </conditional>
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
122
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
123 <!-- Genome source. -->
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
124 <conditional name="fasta_type">
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
125 <param name="fasta_type_selector" type="select" label="Source for sequence to search">
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
126 <option value="cached">Locally Cached sequences</option>
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
127 <option value="history" selected="true">Sequences from your history</option>
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
128 </param>
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
129 <when value="cached">
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
130 <param name="ownFile"
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
131 type="select" label="Genome to search">
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
132 <options from_data_table="all_fasta">
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
133 <column name="dbkey" index="1"/>
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
134 <column name="name" index="2"/>
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
135 <column name="value" index="3"/>
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
136 </options>
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
137 </param>
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
138 </when>
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
139 <when value="history">
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
140 <param name="ownFile"
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
141 type="data"
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
142 format="fasta"
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
143 label="Select the reference genome (FASTA file)"/>
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
144 </when>
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
145 </conditional>
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
146
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
147 <param name="geneModel"
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
148 type="data"
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
149 format="gff3,gtf"
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
150 label="Gene model (gff3,gtf) file for splice junctions and fusion gene detection"/>
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
151 <param name="blast_pairs"
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
152 type="data"
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
153 format="tabular"
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
154 label="Result of BLAST+-blastn of the reference fasta sequence with itself"
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
155 help="Run blastn with '-outputfmt 6' or choose 'Tabular (standard 12 columns)' in the Galaxy wrapper. For human data it is recommended to obtain it from here: https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/"/>
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
156
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
157 <conditional name="params">
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
158 <param name="settingsType" type="select" label="Settings to use" help="You can use the default settings or set custom values for any STAR Fusion parameter.">
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
159 <option value="default" selected="true">Use Defaults</option>
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
160 <option value="full">Full parameter list</option>
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
161 </param>
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
162 <when value="default" />
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
163 <when value="full"><!-- Full/advanced params. -->
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
164 <param name="min_junction_reads"
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
165 type="integer" value="1"
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
166 label="minimum number of junction-spanning reads required."
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
167 argument="--min_junction_reads"/>
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
168 <param name="min_sum_frags"
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
169 type="integer"
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
170 value="2"
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
171 label="minimum fusion support = (#junction_reads + #spanning_frags)"
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
172 argument="--min_sum_frags"/>
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
173 <param name="max_promiscuity"
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
174 type="integer"
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
175 value="3"
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
176 label="maximum number of partners allowed for a given fusion"
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
177 argument="--max_promiscuity"/>
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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178 <param name="min_novel_junction_support"
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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179 type="integer"
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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180 value="3"
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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181 label="minimum of 3 junction reads required if breakpoint lacks involvement of only reference junctions"
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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182 argument="--min_novel_junction_support"/>
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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183 <param name="min_alt_pct_junction"
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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184 type="float"
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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185 value="10"
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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186 label="10% of the dominant isoform junction support"
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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187 argument="--min_alt_pct_junction"/>
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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188 <param name="aggregate_novel_junction_dist"
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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189 type="integer"
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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190 value="5"
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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191 label="non-ref junctions within 5 are merged into single calls"
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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192 argument="--aggregate_novel_junction_dist"/>
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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193 <param name="E"
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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194 type="float"
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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195 value="0.001"
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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196 label="E-value threshold for blast searches"
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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197 argument="-E"/>
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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198 </when>
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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199 </conditional>
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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200 </inputs>
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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201
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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202 <outputs>
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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203 <data format="tabular" name="output_final" label="${tool.name} on ${on_string}: fusion_candidates.final" from_work_dir="star-fusion.fusion_candidates.final"/>
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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204 </outputs>
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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205
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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206 <tests>
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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207 <test>
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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208 <param name="input_source" value="use_chimeric" />
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
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209 <param name="chimeric_junction" ftype="interval" value="test1.tabular" />
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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210 <param name="fasta_type_selector" value="history" />
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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211 <param name="ownFile" ftype="fasta" value="test1.fa" />
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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212 <param name="geneModel" ftype="gtf" value="test1.gtf" />
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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213 <param name="blast_pairs" ftype="tabular" value="test1-test1.blastn.tabular" />
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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214 <param name="settingsType" value="default" />
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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215
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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216 <!-- Last column of the results contains data in a random order so exact matching is not feasible -->
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
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diff changeset
217 <output name="output_final">
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
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218 <assert_contents>
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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219 <has_line line="#fusion_name&#009;JunctionReads&#009;SpanningFrags&#009;Splice_type&#009;LeftGene&#009;LeftBreakpoint&#009;RightGene&#009;RightBreakpoint&#009;JunctionReads&#009;SpanningFrags" />
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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220 <has_text text="GENE1--GENE2&#009;24&#009;0&#009;INCL_NON_REF_SPLICE&#009;GENE1^GENE1&#009;chr1:240:+&#009;GENE2^GENE2&#009;chr2:241:+" />
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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diff changeset
221 </assert_contents>
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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222 </output>
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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223 </test>
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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224 <test>
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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225 <param name="input_source" value="use_fastq" />
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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226 <param name="left_fq" ftype="fastqsanger" value="test1.fastqsanger"/>
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
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227 <param name="fasta_type_selector" value="history" />
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
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228 <param name="ownFile" ftype="fasta" value="test1.fa" />
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
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229 <param name="geneModel" ftype="gtf" value="test1.gtf" />
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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230 <param name="blast_pairs" ftype="tabular" value="test1-test1.blastn.tabular" />
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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231 <param name="settingsType" value="default" />
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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232
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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233 <!-- Last column of the results contains data in a random order so exact matching is not feasible -->
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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234 <output name="output_final">
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
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235 <assert_contents>
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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236 <has_line line="#fusion_name&#009;JunctionReads&#009;SpanningFrags&#009;Splice_type&#009;LeftGene&#009;LeftBreakpoint&#009;RightGene&#009;RightBreakpoint&#009;JunctionReads&#009;SpanningFrags" />
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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237 <has_text text="GENE1--GENE2&#009;24&#009;0&#009;INCL_NON_REF_SPLICE&#009;GENE1^GENE1&#009;chr1:240:+&#009;GENE2^GENE2&#009;chr2:241:+" />
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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238 </assert_contents>
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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239 </output>
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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240 </test>
1
f2c3551338f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit d6a7537117d814677113ba9a8e4783a80dd228a2
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241 <test>
f2c3551338f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit d6a7537117d814677113ba9a8e4783a80dd228a2
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242 <param name="input_source" value="use_fastq" />
f2c3551338f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit d6a7537117d814677113ba9a8e4783a80dd228a2
iuc
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243 <param name="left_fq" ftype="fastqsanger.gz" value="test1.fastqsanger.gz"/>
f2c3551338f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit d6a7537117d814677113ba9a8e4783a80dd228a2
iuc
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244 <param name="fasta_type_selector" value="history" />
f2c3551338f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit d6a7537117d814677113ba9a8e4783a80dd228a2
iuc
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245 <param name="ownFile" ftype="fasta" value="test1.fa" />
f2c3551338f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit d6a7537117d814677113ba9a8e4783a80dd228a2
iuc
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246 <param name="geneModel" ftype="gtf" value="test1.gtf" />
f2c3551338f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit d6a7537117d814677113ba9a8e4783a80dd228a2
iuc
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247 <param name="blast_pairs" ftype="tabular" value="test1-test1.blastn.tabular" />
f2c3551338f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit d6a7537117d814677113ba9a8e4783a80dd228a2
iuc
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248 <param name="settingsType" value="default" />
f2c3551338f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit d6a7537117d814677113ba9a8e4783a80dd228a2
iuc
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diff changeset
249
f2c3551338f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit d6a7537117d814677113ba9a8e4783a80dd228a2
iuc
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diff changeset
250 <!-- Last column of the results contains data in a random order so exact matching is not feasible -->
f2c3551338f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit d6a7537117d814677113ba9a8e4783a80dd228a2
iuc
parents: 0
diff changeset
251 <output name="output_final">
f2c3551338f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit d6a7537117d814677113ba9a8e4783a80dd228a2
iuc
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diff changeset
252 <assert_contents>
f2c3551338f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit d6a7537117d814677113ba9a8e4783a80dd228a2
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253 <has_line line="#fusion_name&#009;JunctionReads&#009;SpanningFrags&#009;Splice_type&#009;LeftGene&#009;LeftBreakpoint&#009;RightGene&#009;RightBreakpoint&#009;JunctionReads&#009;SpanningFrags" />
f2c3551338f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit d6a7537117d814677113ba9a8e4783a80dd228a2
iuc
parents: 0
diff changeset
254 <has_text text="GENE1--GENE2&#009;24&#009;0&#009;INCL_NON_REF_SPLICE&#009;GENE1^GENE1&#009;chr1:240:+&#009;GENE2^GENE2&#009;chr2:241:+" />
f2c3551338f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit d6a7537117d814677113ba9a8e4783a80dd228a2
iuc
parents: 0
diff changeset
255 </assert_contents>
f2c3551338f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit d6a7537117d814677113ba9a8e4783a80dd228a2
iuc
parents: 0
diff changeset
256 </output>
f2c3551338f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit d6a7537117d814677113ba9a8e4783a80dd228a2
iuc
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257 </test>
0
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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258 </tests>
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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259 <help>
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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260 **What it does**
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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261
632b90370be0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
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262 STAR-Fusion is a component of the Trinity Cancer Transcriptome Analysis Toolkit (CTAT). STAR-Fusion uses the STAR aligner to identify candidate fusion transcripts supported by Illumina reads. STAR-Fusion further processes the output generated by the STAR aligner to map junction reads and spanning reads to a reference annotation set.
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263
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264 **Input: files required to run STAR-Fusion**
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265 - A genome reference sequence (FASTA-format)
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266 - A corresponding protein-coding gene annotation set (GTF/GFF Format)
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267 - A last-matching gene pairs file - in Galaxy you can create such files with the *ncbi_blast_plus* tool suite containing *blastn*: https://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus
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268 - A STAR chimeric/junction output file - this is optional as STAR Fusion can control running STAR as well.
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269
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270 The authors of STAR Fusion have made some of these files avaialble at: https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/. The gene annotations in each case are restricted to the protein-coding and lincRNA transcripts.
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271 More info: https://github.com/STAR-Fusion/STAR-Fusion/wiki
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272
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273 </help>
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274
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275 <citations>
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276 <citation type="bibtex">
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277 @unpublished{star_fusion,
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278 author = {Brian Haas and Nicolas Stransky and Daniel Nicorici},
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279 title = {STAR-Fusion},
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280 url = {https://github.com/STAR-Fusion/STAR-Fusion}
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281 }
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282 </citation>
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283 </citations>
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284 </tool>