annotate star_fusion.xml @ 3:137942fac417 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit 7e10d9499da95a5011936d0650810687a66574dd"
author iuc
date Mon, 06 Jan 2020 11:08:46 -0500
parents 0b44456754e2
children
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1 <tool id="star_fusion" name="STAR-Fusion" version="0.5.4-3+galaxy1" profile="17.01">
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2 <description>detect fusion genes in RNA-Seq data</description>
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3 <requirements>
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4 <requirement type="package" version="0.5.4">star-fusion</requirement>
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5 </requirements>
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7 <stdio>
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8 <regex match="command not found" source="stderr" level="fatal"/>
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9 <regex match="EXITING because of INPUT ERROR" source="stderr" level="fatal"/>
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10 <regex match="FATAL ERROR" source="stderr" level="fatal"/>
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12 <regex match="Warning:" source="stderr" level="warning"/>
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13 <regex match="CMD:" source="stderr" level="warning"/>
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93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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15 <regex match="-done creating index file:" source="stderr" level="warning"/>
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16 <regex match="-parsing GTF file:" source="stderr" level="warning"/>
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17 <regex match="-building interval tree" source="stderr" level="warning"/>
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18 <regex match="-parsing fusion evidence:" source="stderr" level="warning"/>
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19 <regex match="-mapping reads to genes" source="stderr" level="warning"/>
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20 <regex match="-outputting fusion candidates to file:" source="stderr" level="warning"/>
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22 <regex match="Process complete" source="stderr" level="warning"/>
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23 </stdio>
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25 <version_command>STAR-Fusion --version 2>&amp;1 | grep version | grep -o -E "software version.*?"</version_command>
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93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
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27 <command><![CDATA[
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28 ## 1. ensure the blastn file is provided as *.gz
137942fac417 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit 7e10d9499da95a5011936d0650810687a66574dd"
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29 gzip -1 -c -- '${blast_pairs}' > blast_pairs.gz &&
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30
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31 ## 2. create reference index - using \$(pwd) is necessary, probably because the perl script changes work directory
137942fac417 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit 7e10d9499da95a5011936d0650810687a66574dd"
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32 ## - @todo once write a decent STAR and STAR Fusion data manager
137942fac417 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit 7e10d9499da95a5011936d0650810687a66574dd"
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33 prep_genome_lib.pl
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34 --genome_fa '${fasta_type.ownFile}'
137942fac417 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit 7e10d9499da95a5011936d0650810687a66574dd"
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35 --gtf '${geneModel}'
137942fac417 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit 7e10d9499da95a5011936d0650810687a66574dd"
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36 --blast_pairs blast_pairs.gz
137942fac417 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit 7e10d9499da95a5011936d0650810687a66574dd"
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37 --CPU \${GALAXY_SLOTS:-1}
137942fac417 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit 7e10d9499da95a5011936d0650810687a66574dd"
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38 --output_dir "\$(pwd)/tmp_star_fusion_genome_dir"
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39 &&
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41 ## Link in fastq files so they have appropriate extensions
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42 #if str($input_params.input_source) != "use_chimeric":
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43 #if $input_params.left_fq.is_of_type("fastq.gz"):
137942fac417 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit 7e10d9499da95a5011936d0650810687a66574dd"
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44 #set read1 = 'input_1.fastq.gz'
137942fac417 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit 7e10d9499da95a5011936d0650810687a66574dd"
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45 #else:
137942fac417 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit 7e10d9499da95a5011936d0650810687a66574dd"
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46 #set read1 = 'input_1.fastq'
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47 #end if
137942fac417 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit 7e10d9499da95a5011936d0650810687a66574dd"
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48 ln -f -s '${input_params.left_fq}' ${read1} &&
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49
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50 #if $input_params.right_fq:
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51 #if $input_params.right_fq.is_of_type("fastq.gz"):
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52 #set read2 = 'input_2.fastq.gz'
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53 #else:
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54 #set read2 = 'input_2.fastq'
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55 #end if
3
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56 ln -f -s '${input_params.right_fq}' ${read2} &&
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57 #end if
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58 #end if
0
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59
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60 ## 3. Run STAR-Fusion
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61 STAR-Fusion
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62 #if str($input_params.input_source) == "use_chimeric":
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63 --chimeric_junction '${input_params.chimeric_junction}'
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64 #else:
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65 --left_fq ${read1}
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66 #if $input_params.right_fq:
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67 --right_fq ${read2}
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68 #end if
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69 #end if
0
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70
3
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71 --genome_lib_dir "\$(pwd)/tmp_star_fusion_genome_dir"
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72
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73 #if str($params.settingsType) == "full":
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74 --min_junction_reads $params.min_junction_reads
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75 --min_sum_frags $params.min_sum_frags
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76 --max_promiscuity $params.max_promiscuity
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77 --min_novel_junction_support $params.min_novel_junction_support
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78 --min_alt_pct_junction $params.min_alt_pct_junction
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79 --aggregate_novel_junction_dist $params.aggregate_novel_junction_dist
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80 --E $params.E
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81 #end if
0
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82 ]]></command>
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83
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84 <inputs>
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85 <conditional name="input_params">
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86 <param name="input_source"
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87 type="select"
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88 label="Use output from earlier STAR run or let STAR Fusion control running STAR">
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89 <option value="use_chimeric">Use output from earlier STAR</option>
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
90 <option value="use_fastq">Let STAR Fusion control running STAR</option>
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
91 </param>
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
92 <when value="use_chimeric">
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
93 <param name="chimeric_junction"
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
94 type="data"
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
95 format="interval"
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
96 argument="--chimeric_junction"
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
97 label="Chimeric junction file from STAR (with STAR-Fusion settings)"/>
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
98 </when>
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
99 <when value="use_fastq">
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
100 <param name="left_fq"
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
101 type="data"
1
0b44456754e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit d6a7537117d814677113ba9a8e4783a80dd228a2
iuc
parents: 0
diff changeset
102 format="fastqsanger,fastqsanger.gz"
0
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
103 argument="--left_fq"
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
104 label="left.fq file"/>
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
105 <param name="right_fq"
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
106 type="data"
1
0b44456754e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit d6a7537117d814677113ba9a8e4783a80dd228a2
iuc
parents: 0
diff changeset
107 format="fastqsanger,fastqsanger.gz"
0
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
108 optional="true"
93704f98f56e 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 argument="--right_fq"
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
110 label="right.fq file (actually optional, but highly recommended)"/>
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
111 </when>
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
112 </conditional>
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
113
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
114 <!-- Genome source. -->
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
115 <conditional name="fasta_type">
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
116 <param name="fasta_type_selector" type="select" label="Source for sequence to search">
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
117 <option value="cached">Locally Cached sequences</option>
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
118 <option value="history" selected="true">Sequences from your history</option>
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
119 </param>
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
120 <when value="cached">
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
121 <param name="ownFile"
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
122 type="select" label="Genome to search">
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
123 <options from_data_table="all_fasta">
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
124 <column name="dbkey" index="1"/>
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
125 <column name="name" index="2"/>
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
126 <column name="value" index="3"/>
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
127 </options>
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
128 </param>
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
129 </when>
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
130 <when value="history">
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
131 <param name="ownFile"
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
132 type="data"
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
133 format="fasta"
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
134 label="Select the reference genome (FASTA file)"/>
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
135 </when>
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
136 </conditional>
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
137
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
138 <param name="geneModel"
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
139 type="data"
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
140 format="gff3,gtf"
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
141 label="Gene model (gff3,gtf) file for splice junctions and fusion gene detection"/>
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
142 <param name="blast_pairs"
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
143 type="data"
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
144 format="tabular"
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
145 label="Result of BLAST+-blastn of the reference fasta sequence with itself"
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
146 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/"/>
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
147
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
148 <conditional name="params">
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
149 <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.">
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
150 <option value="default" selected="true">Use Defaults</option>
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
151 <option value="full">Full parameter list</option>
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
152 </param>
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
153 <when value="default" />
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
154 <when value="full"><!-- Full/advanced params. -->
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
155 <param name="min_junction_reads"
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
156 type="integer" value="1"
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
157 label="minimum number of junction-spanning reads required."
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
158 argument="--min_junction_reads"/>
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
159 <param name="min_sum_frags"
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
160 type="integer"
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
161 value="2"
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
162 label="minimum fusion support = (#junction_reads + #spanning_frags)"
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
163 argument="--min_sum_frags"/>
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
164 <param name="max_promiscuity"
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
165 type="integer"
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
166 value="3"
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
167 label="maximum number of partners allowed for a given fusion"
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
168 argument="--max_promiscuity"/>
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
169 <param name="min_novel_junction_support"
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
170 type="integer"
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
171 value="3"
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
172 label="minimum of 3 junction reads required if breakpoint lacks involvement of only reference junctions"
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
173 argument="--min_novel_junction_support"/>
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
174 <param name="min_alt_pct_junction"
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
175 type="float"
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
176 value="10"
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
diff changeset
177 label="10% of the dominant isoform junction support"
93704f98f56e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
iuc
parents:
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178 argument="--min_alt_pct_junction"/>
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179 <param name="aggregate_novel_junction_dist"
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180 type="integer"
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181 value="5"
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182 label="non-ref junctions within 5 are merged into single calls"
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183 argument="--aggregate_novel_junction_dist"/>
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184 <param name="E"
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185 type="float"
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186 value="0.001"
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187 label="E-value threshold for blast searches"
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188 argument="-E"/>
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189 </when>
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190 </conditional>
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191 </inputs>
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192
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193 <outputs>
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194 <data format="tabular" name="output_final" label="${tool.name} on ${on_string}: fusion_candidates.final" from_work_dir="star-fusion.fusion_candidates.final"/>
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195 </outputs>
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196
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197 <tests>
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198 <test>
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199 <param name="input_source" value="use_chimeric" />
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200 <param name="chimeric_junction" ftype="interval" value="test1.tabular" />
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201 <param name="fasta_type_selector" value="history" />
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202 <param name="ownFile" ftype="fasta" value="test1.fa" />
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203 <param name="geneModel" ftype="gtf" value="test1.gtf" />
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204 <param name="blast_pairs" ftype="tabular" value="test1-test1.blastn.tabular" />
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205 <param name="settingsType" value="default" />
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206
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207 <!-- Last column of the results contains data in a random order so exact matching is not feasible -->
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208 <output name="output_final">
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209 <assert_contents>
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210 <has_line line="#fusion_name&#009;JunctionReads&#009;SpanningFrags&#009;Splice_type&#009;LeftGene&#009;LeftBreakpoint&#009;RightGene&#009;RightBreakpoint&#009;JunctionReads&#009;SpanningFrags" />
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211 <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:+" />
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212 </assert_contents>
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213 </output>
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214 </test>
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215 <test>
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216 <param name="input_source" value="use_fastq" />
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217 <param name="left_fq" ftype="fastqsanger" value="test1.fastqsanger"/>
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218 <param name="fasta_type_selector" value="history" />
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219 <param name="ownFile" ftype="fasta" value="test1.fa" />
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220 <param name="geneModel" ftype="gtf" value="test1.gtf" />
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221 <param name="blast_pairs" ftype="tabular" value="test1-test1.blastn.tabular" />
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222 <param name="settingsType" value="default" />
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223
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224 <!-- Last column of the results contains data in a random order so exact matching is not feasible -->
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225 <output name="output_final">
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226 <assert_contents>
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227 <has_line line="#fusion_name&#009;JunctionReads&#009;SpanningFrags&#009;Splice_type&#009;LeftGene&#009;LeftBreakpoint&#009;RightGene&#009;RightBreakpoint&#009;JunctionReads&#009;SpanningFrags" />
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228 <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:+" />
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229 </assert_contents>
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230 </output>
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231 </test>
1
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232 <test>
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233 <param name="input_source" value="use_fastq" />
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234 <param name="left_fq" ftype="fastqsanger.gz" value="test1.fastqsanger.gz"/>
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235 <param name="fasta_type_selector" value="history" />
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236 <param name="ownFile" ftype="fasta" value="test1.fa" />
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237 <param name="geneModel" ftype="gtf" value="test1.gtf" />
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238 <param name="blast_pairs" ftype="tabular" value="test1-test1.blastn.tabular" />
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239 <param name="settingsType" value="default" />
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240
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241 <!-- Last column of the results contains data in a random order so exact matching is not feasible -->
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242 <output name="output_final">
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243 <assert_contents>
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244 <has_line line="#fusion_name&#009;JunctionReads&#009;SpanningFrags&#009;Splice_type&#009;LeftGene&#009;LeftBreakpoint&#009;RightGene&#009;RightBreakpoint&#009;JunctionReads&#009;SpanningFrags" />
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245 <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:+" />
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246 </assert_contents>
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247 </output>
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248 </test>
0
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249 </tests>
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250 <help>
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251 **What it does**
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252
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253 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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254
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255 **Input: files required to run STAR-Fusion**
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256 - A genome reference sequence (FASTA-format)
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257 - A corresponding protein-coding gene annotation set (GTF/GFF Format)
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258 - 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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259 - A STAR chimeric/junction output file - this is optional as STAR Fusion can control running STAR as well.
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260
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261 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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262 More info: https://github.com/STAR-Fusion/STAR-Fusion/wiki
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263
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264 </help>
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265
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266 <citations>
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267 <citation type="bibtex">
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268 @unpublished{star_fusion,
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269 author = {Brian Haas and Nicolas Stransky and Daniel Nicorici},
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270 title = {STAR-Fusion},
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271 url = {https://github.com/STAR-Fusion/STAR-Fusion}
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272 }
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273 </citation>
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274 </citations>
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275 </tool>