Mercurial > repos > badger > trinityrnaseq
annotate trinityrnaseq.xml @ 5:a67c0a0d24ac draft
Update samtools tool_dependency
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Mon, 11 Nov 2013 11:15:53 -0600 |
| parents | d5580071d910 |
| children | 09c1e388c20c |
| rev | line source |
|---|---|
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a34ce2b18877
Update tool_dependencies to trinityrnaseq_2013_08_14 and add samtools and bowtie
Jim Johnson <jj@umn.edu>
parents:
0
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changeset
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1 <tool id="trinityrnaseq" name="Trinity" version="0.0.2"> |
| 0 | 2 <!-- Written by Jeremy Goecks, now maintained here by bhaas --> |
| 3 <description>De novo assembly of RNA-Seq data Using Trinity</description> | |
| 4 <requirements> | |
|
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a34ce2b18877
Update tool_dependencies to trinityrnaseq_2013_08_14 and add samtools and bowtie
Jim Johnson <jj@umn.edu>
parents:
0
diff
changeset
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5 <requirement type="package" version="2013_08_14">trinityrnaseq</requirement> |
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a34ce2b18877
Update tool_dependencies to trinityrnaseq_2013_08_14 and add samtools and bowtie
Jim Johnson <jj@umn.edu>
parents:
0
diff
changeset
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6 <requirement type="package" version="0.1.18">samtools</requirement> |
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a34ce2b18877
Update tool_dependencies to trinityrnaseq_2013_08_14 and add samtools and bowtie
Jim Johnson <jj@umn.edu>
parents:
0
diff
changeset
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7 <requirement type="package" version="1.0.0">bowtie</requirement> |
| 0 | 8 </requirements> |
| 9 <command> | |
| 10 Trinity.pl --JM $JM --CPU $CPU | |
| 11 | |
| 12 ## Inputs. | |
| 13 #if str($inputs.paired_or_single) == "paired": | |
| 14 --left $inputs.left_input --right $inputs.right_input | |
| 15 #if $inputs.left_input.ext == 'fa': | |
| 16 --seqType fa | |
| 17 #else: | |
| 18 --seqType fq | |
| 19 #end if | |
| 20 #if str($inputs.library_type) != "None": | |
| 21 --SS_lib_type $inputs.library_type | |
| 22 #end if | |
| 23 --group_pairs_distance $inputs.group_pairs_distance | |
| 24 #else: | |
| 25 --single $inputs.input | |
| 26 #if str($inputs.input.ext) == 'fa': | |
| 27 --seqType fa | |
| 28 #else: | |
| 29 --seqType fq | |
| 30 #end if | |
| 31 #if str($inputs.library_type) != "None": | |
| 32 --SS_lib_type $inputs.library_type | |
| 33 #end if | |
| 34 #end if | |
| 35 | |
| 36 ## Additional parameters. | |
| 37 #if str($additional_params.use_additional) == "yes": | |
| 38 --min_kmer_cov $additional_params.min_kmer_cov --max_reads_per_graph $additional_params.max_reads_per_graph --bflyHeapSpaceMax $additional_params.bflyHeapSpaceMax | |
| 39 #if $additional_params.bfly_opts != 'None': | |
| 40 --bfly_opts " $additional_params.bfly_opts " | |
| 41 #end if | |
| 42 #end if | |
|
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d5580071d910
Update commandline to detect successful completion
Jim Johnson <jj@umn.edu>
parents:
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43 |
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d5580071d910
Update commandline to detect successful completion
Jim Johnson <jj@umn.edu>
parents:
3
diff
changeset
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44 ## direct output to the log file |
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d5580071d910
Update commandline to detect successful completion
Jim Johnson <jj@umn.edu>
parents:
3
diff
changeset
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45 | tee $trinity_log |
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d5580071d910
Update commandline to detect successful completion
Jim Johnson <jj@umn.edu>
parents:
3
diff
changeset
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46 ## Check output for success message (direct grep output to dev null, -q option quits early leaving tee error messages) |
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d5580071d910
Update commandline to detect successful completion
Jim Johnson <jj@umn.edu>
parents:
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47 | grep 'All commands completed successfully.' > /dev/null |
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d5580071d910
Update commandline to detect successful completion
Jim Johnson <jj@umn.edu>
parents:
3
diff
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48 ## Print the stats to output to provide info on galaxy history item |
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Jim Johnson <jj@umn.edu>
parents:
3
diff
changeset
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49 && \$TRINITY_HOME/util/TrinityStats.pl trinity_out_dir/Trinity.fasta |
| 0 | 50 </command> |
| 51 <inputs> | |
| 52 <param name="JM" type="select" label="JM" help="Amount of memory to allocate to Jellyfish for Kmer catalog construction"> | |
| 53 <option value="1G">1G</option> | |
| 54 <option value="10G">10G</option> | |
| 55 <option value="50G">50G</option> | |
| 56 <option value="100G">100G</option> | |
| 57 <option value="200G">200G</option> | |
| 58 <option value="500G">500G</option> | |
| 59 </param> | |
| 60 | |
| 61 <param name="CPU" type="integer" value="2" min="1" label="CPU" help="Number of CPUs to use by Trinity" /> | |
| 62 | |
| 63 | |
| 64 <conditional name="inputs"> | |
| 65 <param name="paired_or_single" type="select" label="Paired or Single-end data?"> | |
| 66 <option value="paired">Paired</option> | |
| 67 <option value="single">Single</option> | |
| 68 </param> | |
| 69 <when value="paired"> | |
| 70 <param format="fasta,fastq" name="left_input" type="data" label="Left/Forward strand reads" help=""/> | |
| 71 <param format="fasta,fastq" name="right_input" type="data" label="Right/Reverse strand reads" help=""/> | |
| 72 <param name="library_type" type="select" label="Strand-specific Library Type"> | |
| 73 <option value="None">None</option> | |
| 74 <option value="FR">FR</option> | |
| 75 <option value="RF">RF</option> | |
| 76 </param> | |
| 77 <param name="group_pairs_distance" type="integer" value="500" min="1" label="Group pairs distance" help="Maximum length expected between fragment pairs"/> | |
| 78 <param name="path_reinforcement_distance" type="integer" value="75" min="1" label="Path reinforcement distance" help="Minimum read overlap required for path extension in the graph" /> | |
| 79 | |
| 80 </when> | |
| 81 <when value="single"> | |
| 82 <param format="fasta,fastq" name="input" type="data" label="Single-end reads" help=""/> | |
| 83 <param name="library_type" type="select" label="Strand-specific Library Type"> | |
| 84 <option value="None">None</option> | |
| 85 <option value="F">F</option> | |
| 86 <option value="R">R</option> | |
| 87 </param> | |
| 88 <param name="path_reinforcement_distance" type="integer" value="40" min="1" label="Path reinforcement distance" help="Minimum read overlap required for path extension in the graph" /> | |
| 89 </when> | |
| 90 </conditional> | |
| 91 | |
| 92 <conditional name="additional_params"> | |
| 93 <param name="use_additional" type="select" label="Use Additional Params?"> | |
| 94 <option value="no">No</option> | |
| 95 <option value="yes">Yes</option> | |
| 96 </param> | |
| 97 <when value="no"> | |
| 98 </when> | |
| 99 <when value="yes"> | |
| 100 <param name="min_kmer_cov" type="integer" value="1" min="1" label="inchworm_min_kmer_cov" help="Minimum kmer coverage required by Inchworm for initial contig construction" /> | |
| 101 <param name="max_reads_per_graph" type="integer" value="20000000" min="10000" label="chrysalis_max_reads_per_graph" help="Maximum number of reads to be anchored within each transcript graph by Chrysalis" /> | |
| 102 <param name="bfly_opts" type="text" value="None" label="bfly_opts" help="Options to pass on to Butterfly" /> | |
| 103 <param name="bflyHeapSpaceMax" type="select" label="bflyHeapSpaceMax" help="Java heap space maximum value for Butterfly"> | |
| 104 <option value="1G">1G</option> | |
| 105 <option value="2G">2G</option> | |
| 106 <option value="4G" selected="true">4G</option> | |
| 107 <option value="10G">10G</option> | |
| 108 <option value="20G">20G</option> | |
| 109 </param> | |
| 110 <param name="min_contig_length" type="integer" value="200" min="1" label="Minimum Contig Length" help=""/> | |
| 111 </when> | |
| 112 </conditional> | |
| 113 </inputs> | |
| 114 <stdio> | |
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Add trinityrnaseq_norm and transcriptsToOrfs tools
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115 <exit_code range="1:" level="fatal" description="Failed" /> |
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a34ce2b18877
Update tool_dependencies to trinityrnaseq_2013_08_14 and add samtools and bowtie
Jim Johnson <jj@umn.edu>
parents:
0
diff
changeset
|
116 <regex match="command not found" |
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a34ce2b18877
Update tool_dependencies to trinityrnaseq_2013_08_14 and add samtools and bowtie
Jim Johnson <jj@umn.edu>
parents:
0
diff
changeset
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117 source="both" |
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a34ce2b18877
Update tool_dependencies to trinityrnaseq_2013_08_14 and add samtools and bowtie
Jim Johnson <jj@umn.edu>
parents:
0
diff
changeset
|
118 level="fatal" |
|
a34ce2b18877
Update tool_dependencies to trinityrnaseq_2013_08_14 and add samtools and bowtie
Jim Johnson <jj@umn.edu>
parents:
0
diff
changeset
|
119 description="Trinity.pl not found" /> |
| 0 | 120 </stdio> |
| 121 <outputs> | |
| 122 <data format="txt" name="trinity_log" label="${tool.name} on ${on_string}: log" /> | |
| 123 <data format="fasta" name="assembled_transcripts" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir/Trinity.fasta"/> | |
| 124 </outputs> | |
| 125 <tests> | |
| 126 | |
| 127 <test> | |
| 128 <param name="JM" value="1G"/> | |
| 129 <param name="CPU" value="1"/> | |
| 130 <param name="paired_or_single" value="single"/> | |
| 131 <param name="input" ftype="fastq" value="reads.left.fq"/> | |
| 132 <param name="library_type" value="None"/> | |
| 133 <param name="path_reinforcement_distance" value="40"/> | |
| 134 <param name="use_additional" value="no"/> | |
| 135 <output name="trinity_log"> | |
| 136 <assert_contents> | |
| 137 <!-- sequence merged from multiple reads --> | |
| 138 <has_text text="Butterfly assemblies are written to" /> | |
| 139 </assert_contents> | |
| 140 </output> | |
| 141 <output name="assembled_transcripts"> | |
| 142 <assert_contents> | |
| 143 <!-- sequence merged from multiple reads --> | |
| 144 <has_text text="CCATGAGGGGGGGGGGCAATGG" /> | |
| 145 </assert_contents> | |
| 146 </output> | |
| 147 </test> | |
| 148 | |
| 149 <test> | |
| 150 <param name="JM" value="1G"/> | |
| 151 <param name="CPU" value="1"/> | |
| 152 <param name="paired_or_single" value="paired"/> | |
| 153 <param name="left_input" ftype="fastq" value="reads.left.fq"/> | |
| 154 <param name="right_input" ftype="fastq" value="reads.right.fq"/> | |
| 155 <param name="library_type" value="None"/> | |
| 156 <param name="group_pairs_distance" value="500"/> | |
| 157 <param name="path_reinforcement_distance" value="75"/> | |
| 158 <param name="use_additional" value="no"/> | |
| 159 <output name="trinity_log"> | |
| 160 <assert_contents> | |
| 161 <!-- sequence merged from multiple reads --> | |
| 162 <has_text text="Butterfly assemblies are written to" /> | |
| 163 </assert_contents> | |
| 164 </output> | |
| 165 <output name="assembled_transcripts"> | |
| 166 <assert_contents> | |
| 167 <!-- sequence merged from multiple reads --> | |
| 168 <has_text text="AAGCTGGCCTCAAATTCCTGATCC" /> | |
| 169 </assert_contents> | |
| 170 </output> | |
| 171 </test> | |
| 172 </tests> | |
| 173 <help> | |
| 174 Trinity is a de novo transcript assembler that uses RNA-seq data as input. This tool runs all Trinity_ commands--Inchworm, Chrysalis, and Butterfly--in a single pass. | |
| 175 | |
| 176 .. _Trinity: http://trinityrnaseq.sourceforge.net | |
| 177 </help> | |
| 178 </tool> |