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comparison arriba.xml @ 4:77021ad5037d draft

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"planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 5a62e8a2ec56a8ce00f89c8fbe61b3f1dffbbffd"
author jjohnson
date Sat, 09 Oct 2021 15:41:49 +0000
parents 2d32e6c86c48
children 005b200c8841
comparison
equal deleted inserted replaced
3:2d32e6c86c48 4:77021ad5037d
18 #else: 18 #else:
19 #set read2 = 'input_2.fastq' 19 #set read2 = 'input_2.fastq'
20 #end if 20 #end if
21 ln -f -s '${input_params.right_fq}' ${read2} && 21 ln -f -s '${input_params.right_fq}' ${read2} &&
22 #if str($input_params.index.index_source) == "history" 22 #if str($input_params.index.index_source) == "history"
23 #set $star_index_dir = $input_params.index.star_index.files_path 23 #set $star_index_dir = $input_params.index.star_index.extra_files_path
24 #end if 24 #end if
25 STAR 25 STAR
26 --runThreadN \${GALAXY_SLOTS:-1} 26 --runThreadN \${GALAXY_SLOTS:-1}
27 --genomeDir $star_index_dir 27 --genomeDir $star_index_dir
28 --genomeLoad NoSharedMemory 28 --genomeLoad NoSharedMemory
54 -c '$input_params.chimeric' 54 -c '$input_params.chimeric'
55 #end if 55 #end if
56 #end if 56 #end if
57 -a '$genome_assembly' 57 -a '$genome_assembly'
58 -g '$gtf' 58 -g '$gtf'
59 #if '$blacklist' 59 #if $blacklist
60 -b '$blacklist' 60 -b '$blacklist'
61 #end if 61 #else
62 #if '$protein_domains' 62 -f 'blacklist'
63 #end if
64 #if $protein_domains
63 -p '$protein_domains' 65 -p '$protein_domains'
64 #end if 66 #end if
65 #if '$known_fusions' 67 #if $known_fusions
66 -k '$known_fusions' 68 -k '$known_fusions'
67 #end if 69 #end if
68 #if '$tags' 70 #if $tags
69 -t '$tags' 71 -t '$tags'
70 #end if 72 #end if
71 -o fusions.tsv 73 -o fusions.tsv
72 -O fusions.discarded.tsv 74 -O fusions.discarded.tsv
73 #if str($input_params.input_source) == "use_fastq" 75 #if str($input_params.input_source) == "use_fastq"
74 && samtools sort -@ "$THREADS" -m 4G -T tmp -O bam Aligned.out.bam > Aligned.sortedByCoord.out.bam 76 && samtools sort -@ \${GALAXY_SLOTS:-1} -m 4G -T tmp -O bam Aligned.out.bam > Aligned.sortedByCoord.out.bam
75 && samtools index Aligned.sortedByCoord.out.bam 77 && samtools index Aligned.sortedByCoord.out.bam
76 #elif str($visualization.do_viz) == "yes" 78 #elif str($visualization.do_viz) == "yes"
77 && samtools sort -@ "$THREADS" -m 4G -T tmp -O bam '$input_params.input' > Aligned.sortedByCoord.out.bam 79 && samtools sort -@ \${GALAXY_SLOTS:-1} -m 4G -T tmp -O bam '$input_params.input' > Aligned.sortedByCoord.out.bam
78 && samtools index Aligned.sortedByCoord.out.bam 80 && samtools index Aligned.sortedByCoord.out.bam
79 #end if 81 #end if
80 #if str($visualization.do_viz) == "yes" 82 #if str($visualization.do_viz) == "yes"
81 draw_fusions.R \ 83 && draw_fusions.R
82 --fusions=fusions.tsv 84 --fusions=fusions.tsv
83 --alignments=Aligned.sortedByCoord.out.bam 85 --alignments=Aligned.sortedByCoord.out.bam
84 --output=fusions.pdf 86 --output=fusions.pdf
85 --annotation='$gtf' 87 --annotation='$gtf'
86 #if $visualization.cytobands 88 #if $visualization.cytobands
87 --cytobands='$visualization.cytobands' 89 --cytobands='$visualization.cytobands'
88 #end if 90 #end if
89 #if '$protein_domains' 91 #if '$protein_domains'
90 --proteinDomains=database/protein_domains_hg19_hs37d5_GRCh37_v2.1.0.gff3 92 --proteinDomains='$protein_domains'
91 #end if 93 #end if
92 #end if 94 #end if
93 95
94 ]]></command> 96 ]]></command>
95 <inputs> 97 <inputs>
127 </when> 129 </when>
128 </conditional> 130 </conditional>
129 <param name="genome_assembly" argument="-a" type="data" format="fasta" label="genome assembly fasta"/> 131 <param name="genome_assembly" argument="-a" type="data" format="fasta" label="genome assembly fasta"/>
130 <param name="gtf" argument="-g" type="data" format="gtf" label="GTF file with gene annotation"/> 132 <param name="gtf" argument="-g" type="data" format="gtf" label="GTF file with gene annotation"/>
131 <param name="blacklist" argument="-b" type="data" format="tabular" optional="true" label="File containing blacklisted ranges."/> 133 <param name="blacklist" argument="-b" type="data" format="tabular" optional="true" label="File containing blacklisted ranges."/>
132 <param name="protein_domains" argument="-p" type="data" format="gff3" optional="true" label="File containing blacklisted ranges."/> 134 <param name="protein_domains" argument="-p" type="data" format="gff3" optional="true" label="File containing protein domains"/>
133 <param name="known_fusions" argument="-k" type="data" format="tabular" optional="true" label="File containing known fusions"> 135 <param name="known_fusions" argument="-k" type="data" format="tabular" optional="true" label="File containing known fusions">
134 <help><![CDATA[ file two TAB separated columns: five-prime region three-prime region ]]></help> 136 <help><![CDATA[ file two TAB separated columns: five-prime region three-prime region ]]></help>
135 </param> 137 </param>
136 <param name="tags" argument="-t" type="data" format="tabular" optional="true" label="File containing tag names for a fusion."/> 138 <param name="tags" argument="-t" type="data" format="tabular" optional="true" label="File containing tag names for a fusion."
139 help="This can be the known fusions if that input has a third column with a name"/>
137 <conditional name="visualization"> 140 <conditional name="visualization">
138 <param name="do_viz" type="select" label="Generate visualization"> 141 <param name="do_viz" type="select" label="Generate visualization">
139 <option value="yes">Yes</option> 142 <option value="yes">Yes</option>
140 <option value="no">no</option> 143 <option value="no">no</option>
141 </param> 144 </param>
150 <data name="fusions" format="tabular" label="${tool.name} on ${on_string}: fusions.tsv" from_work_dir="fusions.tsv"/> 153 <data name="fusions" format="tabular" label="${tool.name} on ${on_string}: fusions.tsv" from_work_dir="fusions.tsv"/>
151 <data name="discarded" format="tabular" label="${tool.name} on ${on_string}: fusions.discarded.tsv" from_work_dir="fusions.discarded.tsv"/> 154 <data name="discarded" format="tabular" label="${tool.name} on ${on_string}: fusions.discarded.tsv" from_work_dir="fusions.discarded.tsv"/>
152 <data name="aligned_bam" format="bam" label="${tool.name} on ${on_string}: Aligned.bam" from_work_dir="Aligned.sortedByCoord.out.bam"> 155 <data name="aligned_bam" format="bam" label="${tool.name} on ${on_string}: Aligned.bam" from_work_dir="Aligned.sortedByCoord.out.bam">
153 <filter>input_params['input_source'] == "use_fastq"</filter> 156 <filter>input_params['input_source'] == "use_fastq"</filter>
154 </data> 157 </data>
155 <data name="fusions_png" format="png" label="${tool.name} on ${on_string}: fusions.pdf" from_work_dir="fusions.pdf"> 158 <data name="fusions_pdf" format="pdf" label="${tool.name} on ${on_string}: fusions.pdf" from_work_dir="fusions.pdf">
156 <filter>visualization['do_viz'] == "yes"</filter> 159 <filter>visualization['do_viz'] == "yes"</filter>
157 </data> 160 </data>
158 </outputs> 161 </outputs>
162 <tests>
163 <!-- Test 1 - From exisitng BAM -->
164 <test>
165 <conditional name="input_params">
166 <param name="input_source" value="use_star"/>
167 <param name="input" ftype="sam" value="Aligned.out.sam"/>
168 </conditional>
169 <param name="genome_assembly" ftype="fasta" value="genome.fasta"/>
170 <param name="gtf" ftype="gtf" value="genome.gtf"/>
171 <conditional name="visualization">
172 <param name="do_viz" value="no"/>
173 </conditional>
174 <output name="fusions">
175 <assert_contents>
176 <has_text_matching expression="BCR\tABL1"/>
177 </assert_contents>
178 </output>
179 </test>
180 </tests>
159 <help><![CDATA[ 181 <help><![CDATA[
160 ** Arriba ** 182 ** Arriba **
161 183
162 184
163 Arriba_ is a fast tool to search for aberrant transcripts such as gene fusions. 185 Arriba_ is a fast tool to search for aberrant transcripts such as gene fusions.