Mercurial > repos > iuc > trinity

comparison trinity.xml @ 34:8f1c3df4dd49 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit ec26c475a013d89b0f973f29250d660e79d4751f
author iuc
date Wed, 20 Sep 2023 14:54:54 +0000
parents 9fa24d5aac68
children
comparison
equal deleted inserted replaced
33:9fa24d5aac68 34:8f1c3df4dd49
1 <tool id="trinity" name="Trinity" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 1 <tool id="trinity" name="Trinity" version="@TOOL_VERSION@+galaxy1" profile="21.05">
2 <description>de novo assembly of RNA-Seq data</description> 2 <description>de novo assembly of RNA-Seq data</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="bio_tools"/> 6 <expand macro="bio_tools"/>
12 GALAXY_MEMORY_GB=1 ; 12 GALAXY_MEMORY_GB=1 ;
13 else 13 else
14 GALAXY_MEMORY_GB=\$((GALAXY_MEMORY_MB / 1024)) ; 14 GALAXY_MEMORY_GB=\$((GALAXY_MEMORY_MB / 1024)) ;
15 fi ; 15 fi ;
16 16
17 if [ ! -z "\$TRINITY_SCRATCH_DIR" ] ; then 17 TRINITY_SCRATCH_DIR=\${TRINITY_SCRATCH_DIR:-\${TMPDIR:-\$_GALAXY_JOB_TMP_DIR}}
18 workdir=`pwd` ; 18 workdir=\$(pwd)
19 scratchfolder=\$(mktemp -d -p "\$TRINITY_SCRATCH_DIR"); 19 scratchfolder=\$(mktemp -d -p "\$TRINITY_SCRATCH_DIR");
20 emptyfolder=\$(mktemp -d -p "\$TRINITY_SCRATCH_DIR"); 20 emptyfolder=\$(mktemp -d -p "\$TRINITY_SCRATCH_DIR");
21 cd "\$scratchfolder" ; 21 cd "\$scratchfolder" ;
22 fi ;
23 22
24 #if $additional_params.guided.is_guided == "yes": 23 #if $additional_params.guided.is_guided == "yes":
25 ln -s '${$additional_params.guided.genome_guided_bam}' 'localbam.bam' && 24 ln -s '${$additional_params.guided.genome_guided_bam}' 'localbam.bam' &&
26 ln -s '${$additional_params.guided.genome_guided_bam.metadata.bam_index}' 'localbam.bam.bai' && 25 ln -s '${$additional_params.guided.genome_guided_bam.metadata.bam_index}' 'localbam.bam.bai' &&
27 #end if 26 #end if
146 #end if 145 #end if
147 146
148 ## CPU and butterfly options. 147 ## CPU and butterfly options.
149 --CPU \${GALAXY_SLOTS:-4} --max_memory \${GALAXY_MEMORY_GB:-1}G --bflyHeapSpaceMax \${GALAXY_MEMORY_GB:-1}G --bfly_opts '-V 10 --stderr' 148 --CPU \${GALAXY_SLOTS:-4} --max_memory \${GALAXY_MEMORY_GB:-1}G --bflyHeapSpaceMax \${GALAXY_MEMORY_GB:-1}G --bfly_opts '-V 10 --stderr'
150 149
151 ## > $trinity_log 2>&1
152
153 && 150 &&
154 151
155 ## Trinity can create millions of files in the same directory, so the cleaning task makes use of rsync 152 ## Trinity can create millions of files in the same directory, so the cleaning task makes use of rsync
156 ## for ensuring better performances. 153 ## for ensuring better performances.
157 ## see: https://web.archive.org/web/20130929001850/http://linuxnote.net/jianingy/en/linux/a-fast-way-to-remove-huge-number-of-files.html 154 ## see: https://web.archive.org/web/20130929001850/http://linuxnote.net/jianingy/en/linux/a-fast-way-to-remove-huge-number-of-files.html
158 if [ ! -z "\$TRINITY_SCRATCH_DIR" ] ; then 155 rsync -a --delete "\$emptyfolder/" "\$scratchfolder/" --exclude=trinity_out_dir.Trinity.fasta --exclude=trinity_out_dir.Trinity.fasta.gene_trans_map;
159 mkdir -p "\$workdir/trinity_out_dir"; 156 mv "\$scratchfolder/trinity_out_dir.Trinity.fasta" '$assembled_transcripts';
160 cp -p trinity_out_dir/Trinity* "\$workdir/trinity_out_dir"; 157 mv "\$scratchfolder/trinity_out_dir.Trinity.fasta.gene_trans_map" '$gene_to_trans';
161 cd "\$TRINITY_SCRATCH_DIR"; 158 cd "\$workdir";
162 rsync -a --delete "\$emptyfolder/" "\$scratchfolder/"; 159 rmdir "\$emptyfolder" "\$scratchfolder"
163 rmdir "\$emptyfolder" "\$scratchfolder/";
164 cd "\$workdir";
165 fi ;
166
167 ]]></command> 160 ]]></command>
168 <inputs> 161 <inputs>
169 <conditional name="pool"> 162 <conditional name="pool">
170 <param name="pool_mode" type="select" label="Are you pooling sequence datasets?" help="" > 163 <param name="pool_mode" type="select" label="Are you pooling sequence datasets?" help="" >
171 <option value="No">No</option> 164 <option value="No">No</option>
233 help="Experimental feature! Long reads must be in the same orientation as short reads if they are strand specific"/> 226 help="Experimental feature! Long reads must be in the same orientation as short reads if they are strand specific"/>
234 <param argument="--min_kmer_cov" type="integer" optional="true" value="1" min="1" label="Minimum count for K-mers to be assembled"/> 227 <param argument="--min_kmer_cov" type="integer" optional="true" value="1" min="1" label="Minimum count for K-mers to be assembled"/>
235 </section> 228 </section>
236 </inputs> 229 </inputs>
237 <outputs> 230 <outputs>
238 <data name="assembled_transcripts" format="fasta" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir.Trinity.fasta"/> 231 <data name="assembled_transcripts" format="fasta" label="${tool.name} on ${on_string}: Assembled Transcripts"/>
239 <data name="gene_to_trans" format="tabular" label="${tool.name} on ${on_string}: Gene to transcripts map" from_work_dir="trinity_out_dir.Trinity.fasta.gene_trans_map"/> 232 <data name="gene_to_trans" format="tabular" label="${tool.name} on ${on_string}: Gene to transcripts map"/>
240 </outputs> 233 </outputs>
241 <tests> 234 <tests>
242 <test> 235 <test>
243 <param name="pool_mode" value="No" /> 236 <param name="pool_mode" value="No" />
244 <param name="paired_or_single" value="unmerged_paired_collection"/> 237 <param name="paired_or_single" value="unmerged_paired_collection"/>