Mercurial > repos > greg > gene_family_classifier
changeset 0:315440c6fb44 draft
Uploaded
author | greg |
---|---|
date | Fri, 09 Dec 2016 08:45:36 -0500 |
parents | |
children | 8b5a8a3ca9ee |
files | gene_family_classifier.xml plant_tribes_scaffolds.loc.sample test-data/assembly.fasta test-data/transcripts.cleaned.nr.pep tool_data_table_conf.xml.sample |
diffstat | 5 files changed, 222 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gene_family_classifier.xml Fri Dec 09 08:45:36 2016 -0500 @@ -0,0 +1,132 @@ +<tool id="plant_tribes_gene_family_classifier" name="PlantTribes GeneFamilyClassifier" version="1.0.0"> + <description>pipeline</description> + <requirements> + <requirement type="package" version="0.2">plant_tribes_gene_family_classifier</requirement> + </requirements> + <stdio> + <!-- Anything other than zero is an error --> + <exit_code range="1:" /> + <!-- In case the return code has not been set properly check stderr too --> + <regex match="Error:" /> + <regex match="Exception:" /> + </stdio> + <command> + <![CDATA[ + GeneFamilyClassifier + --proteins "$input" + --scaffold "$scaffold" + --method $method + --classifier $classifier + #if str($options_type.options_type_selector) == 'advanced': + --super_orthogroups $options_type.super_orthogroups + #if str($options_type.single_copy_cond) == 'taxa': + --single_copy_taxa $options_type.single_copy_cond.single_copy_taxa + --taxa_present $options_type.single_copy_cond.taxa_present + #end if + #if str($options_type.create_orthogroup_cond) == 'yes': + --orthogroup_fasta + --coding_sequences "$options_type.create_orthogroup_cond.coding_sequences" + #end if + #end if + --num_threads \${GALAXY_SLOTS:-4} + ]]> + </command> + <inputs> + <param name="input" format="fasta" type="data" label="Amino acids (proteins) sequences fasta file"/> + <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold"> + <options from_data_table="plant_tribes_scaffolds" /> + <validator type="no_options" message="No PlantTribes scaffolds are available. Use the PlantTribes Scaffolds Download Data Manager tool to install and populate the PlantTribes scaffolds data table."/> + </param> + <param name="method" type="select" label="Protein clustering method"> + <option value="gfam" selected="true">GFam</option> + <option value="orthofinder">OrthoFinder</option> + <option value="orthomcl">OrthoMCL</option> + </param> + <param name="classifier" type="select" label="Protein classification method"> + <option value="blastp" selected="true">blastp</option> + <option value="hmmscan">HMMScan</option> + <option value="both">Both blastp and HMMScan</option> + </param> + <conditional name="options_type"> + <param name="options_type_selector" type="select" label="Options Configuration"> + <option value="basic" selected="true">Basic</option> + <option value="advanced">Advanced</option> + </param> + <when value="basic" /> + <when value="advanced"> + <param name="super_orthogroups" type="select" label="SuperOrthogroups MCL clustering" help="blastp e-value matrix between all pairs of orthogroups"> + <option value="min_evalue" selected="true">Minimum e-value</option> + <option value="avg_evalue">Average e-value</option> + </param> + <conditional name="single_copy_cond"> + <param name="single_copy" type="select" label="Select single copy configuration"> + <option value="custom" selected="true">Single copy orthogroup custom</option> + <option value="taxa">Minumum single copy taxa required in orthogroup</option> + </param> + <when value="custom" /> + <when value="taxa"> + <param name="single_copy_taxa" type="integer" value="20" label="Minumum single copy taxa required in orthogroup"/> + <param name="taxa_present" type="integer" value="21" label="Minumum taxa required in single copy orthogroup"/> + </when> + </conditional> + <conditional name="create_orthogroup_cond"> + <param name="create_orthogroup" type="select" label="Create orthogroup fasta files?"> + <option value="no" selected="true">No</option> + <option value="yes">Yes</option> + </param> + <when value="no" /> + <when value="yes"> + <param name="coding_sequences" format="fasta" type="data" label="Corresponding coding sequences (CDS) fasta file"/> + </when> + </conditional> + </when> + </conditional> + </inputs> + <outputs> + <collection name="transcripts" type="list"> + <discover_datasets pattern="__name__" directory="assemblyPostProcessing_dir" visible="false" ext="fasta" /> + </collection> + </outputs> + <tests> + <test> + <param name="input" value="" ftype="fasta" /> + <param name="prediction_method" value="transdecoder"/> + <param name="target_gene_family_assembly" value="no"/> + <param name="strand_specific" value="yes"/> + <param name="dereplicate" value="yes"/> + <param name="min_length" value="200"/> + <output_collection name="orthos" type="list"> + + </output_collection> + </test> + </tests> + <help> +This tool is one of the PlantTribes' collection of automated modular analysis pipelines that utilize objective classifications of +complete protein sequences from sequenced plant genomes to perform comparative evolutionary studies. It performs Gene family +classification of the post processed de novo transcripts using either blastp (faster), HMMScan (slower but more sensitive to remote +homologs) or both (more exhaustive). + +----- + +**Options** + + * **Orthogroups or gene families proteins scaffold** - PlantTribes scaffolds data. + * **Protein clustering method** - One of GFam, OrthoFinder or OrthoMCL. + * **Protein classification method** - One of blastp, HMMScan or both. + * **SuperOrthogroups MCL clustering** - blastp e-value matrix between all pairs of orthogroups. + * **Minumum single copy taxa required in orthogroup** - Used with "Minumum single copy taxa required in orthogroup" configuration only. + * **Minumum taxa required in single copy orthogroup** - Used with "Minumum single copy taxa required in orthogroup" configuration only. + * **Corresponding coding sequences (CDS) fasta file** - Used only when selecting "Create orthogroup fasta files?". + + </help> + <citations> + <citation type="bibtex"> + @unpublished{None, + author = {None}, + title = {None}, + year = {None}, + eprint = {None}, + url = {None} + }</citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/plant_tribes_scaffolds.loc.sample Fri Dec 09 08:45:36 2016 -0500 @@ -0,0 +1,4 @@ +## Plant Tribes scaffolds +#Value Name Path Description +#22Gv1.0 22Gv1.0 /plant_tribes/scaffolds/22Gv1.0 22 plant genomes (Angiosperms clusters, version 1.0; 22Gv1.0) +#22Gv1.1 22Gv1.1 /plant_tribes/scaffolds/22Gv1.1 22 plant genomes (Angiosperms clusters, version 1.1; 22Gv1.1)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/assembly.fasta Fri Dec 09 08:45:36 2016 -0500 @@ -0,0 +1,73 @@ +>contig_1 +CGATTAACCATGTGTACAACATGACCAATTATGGCCGATCTTGCTTGTTCAGGAGTCTCA +CTCATCATTCCAAAATCAAGAAAAGCAAGCTTCCCGTCAGGTGTAGCTAAGAGATTCCCT +GGGTGAGGATCTGCATGAAAATAGCCGTACTCAAGCAGCTGTCGAAGACTGCACTGTATG +CCGGTATTCACCAGATCCAGAACACTGAGCCCTTGACTCTCAACGGCATCTTGCTCATTT +AATTTAACACCTTCAACCCACTCCATTGTTAGCACCTTTCCACTCGTGTAATCCCAGAAA +ATATCTGGGACAAGGATATCTTCCTTGTCTCCATATAATTTTTTAA +>contig_2 +CCTTTCCAAGGTACCCATCCCATCCAACAACATATATGCTATAAATGATAAGAAGTCCCC +GGAAGATGCAGCAGACGACTACGAAAACCGCCTCAAGGAACTCGTCTCCGAAAAAATCAT +ACCCGTTTCAACCATTAGCGGGTTCCCGAAGTTCGACCTCATGTTGCTTGGAATGGGGCC +CGACGGCCATGTGGCCTCTCTTTTCCCTTCTCACATGCAACGCTATGAGAAGGAGAAATG +GGTCACTTTCATAACTGACTCTCCCAAACCGCCTCCGTCGAGAATCACTTTTACGTTTCC +GATGATCAACTCGGCTTCGGAGATCGCTATGGTGGTTACCGGGGCTGATTTGGCTGGTAC +AACTAAGATAGCATTGGGTACTACGGGCAATGTTAAGCCGGGTGAGACTCCTTTGCCTTG +TACTGAAGTTTCGGCTGAGGGAGAGGTTACTTGGTTCTTGGACAAAGATGCTGCTTCACA +ACTGTTAAATTATGTGCGCTTTGATGATTAAAAACACGGGGTAATTGAACTCAAGGGATG +GTTGAGAATTGTAATATTTCTGTAAGTGTCGGGGGATGGTTGAAATGCTTTTTATTATGA +AGTGTTAAAATGTAAGATAAA +>contig_3 +CGGGGGCAAGGTTTACATGAAAGTACATCTACAGGACCTAGATAAGCATCATCACCTGAC +AAAAAGCCATACATAGTAACACTTGCTAGTTGATCTGTGAAAATGGTGCACGAGTCGTAA +CAGACGGCATTAGTTCCTTTCCTGTAACAGCAGATTCGTATGAATGGTTTTCTCGAAATT +CTTCTTCAAGTGCATCTATAGGCATGGCACGAAGTGACTCTATTGTGCCTTTGCTGGGAA +TATCCGGCTCGCTCCTAACTGGCGTGGACCCTGTAGGCTCGTAATCCATGTATTTTTGCC +TGAAAGTATCATTCGTGTGCTGTTCGATACAGGATACCTGCTGGGAATGATCTCTCTTAA +GGTTCTCAATTGTTTCTGAATGAGCTCTAGCAGTTGTCAGAATTTCAGAAACAGATGCCT +TCTCCTGCTCTGACAAGCCAGCAACAACAACTCCTTCATCCACA +>contig_4 +CTGACGATGTTCATATTCATGCCACTCTAAATGTATGCCATCCATGTTGAGGAGAAATGC +TTGTGTAAAGAAGAAACTGGAGTCAAGCGGTCCCGGTTTTACAGTTGAACGTTGCTCTAA +ATTAGTCAAAGTACCCGACTACCCGCTCATCAAACTGGCGAGCTCGTTTTCCTCGCCGCC +CTACTCGGTGTCTTGGCGGGGCACATGGGGGTGGCGTGTGGCGTGCGGGGATGCGACAAC +ATCATAAATTCATAATCGAAGG +>contig_5 +GTGAGAGTGTCGCCTTTTCCATGCTACCCCTTTCCAGATCTGACTTGTTCGAACCTTCCA +TCATCCGGTTCGACGTCAGCAGTCGGTCCTTCTTCTCCAAGCACGAGAGCAGACGGTGCG +AGAGCGAGCAAAGACTCGCCTGCCGCGCCTCTCGTGACCTGGCTCGCATCTCCAGGATTC +ATGGCTCCTTAGCTCGCCCTTCTTCGATACTTCGCTAGACGCCCGAGGACGTCATCGAAG +GCGAGGGTCGGCACAACGGAGTGCTCCTTGCATGATGTCGGGGCCTGGCATCACGCGGCA +TCGGCCAAATCGTCCCTCTCGACGTGCGTCACGGAGAGGGCCGAGCGCCGGGACGACCGC +GTGGAAGAGCCCGCGGGATGCGGGATCCCGCTTGACGTGTGTTTGTGGCGGACCACCG +>contig_6 +TATAACAATTCAAAATATTCCTATGAAAACCAAGACCAGAGGCAACACCGGTATAACCAA +AGCCAGAGGCAATATCCCTTTATTCTTCGGGAACAGAAAAATACACGATATGCTACAGAC +AAAAAAATAAATCCAAACCATTCTTCTGTGCATAAACATTGTAAAAGTTTATTAGACCGC +TGTAAAACTCGTAAATGAAATCCCTGGCAATTGAATCTGTTAAACCTGCTCC +>contig_7 +GAGAATGAGTGGTCTGGGGCTGAGTTTTTGAATGAAATGGCGGCAATGATGACTCAAAAT +AAATCCAATGAAAACGGAACCGGAACTTTTGAAGAACTGCAACAATTGTTCGATGAAATG +TTTCAGAGCGACATCGAGTCCTTCAATGGTTGTTCTTCATCATCCAATGAAACATGTAGC +AACTCGAACAAGAGGAATTCCATTGAGTCGAGCTCGGCTAATTTCAGACCCGAAAATGCG +AAACGAAAGCGGCGAGATTAGCGGGAAGAAGAATACTAGGAAAGGTAAAGGTGACG +>contig_8 +TGGCATGAAGTCGGCTCGACTCGTGCCCGCTCGTCTATAGACGAATTGAGCTAGATTCAC +TCATTCCATGAACTCGACTCGTTCATGAGTCGGCTCGTAGTTGTCCGGACTCGCTCCATG +GCCAGCTCTACAACAGACTGCCTGTATGTAGATGATTGTATTGATTTGTTCTTCTCTTGT +TTAAATCCAACCAAATATCAACATGATATTTGCAATTTC +>contig_9 +ACTTCGGTTAAAGGCAGATGAGGAGGCACAATGTTTGAATCAGATGCAGCGTATCATTTT +TGATGAAATTATGGAGCATGTGGAGTTAGAAAAGGGGGGCTTCTATTTCGTATATCGCCC +TGGGGGCAACGGAAAGACCTTGTGGTTGGCTATTATCTCAAAACTGAGAAGCGAGGGTAG +AATAGTTCTCGCAGTGGCTTCATCAGGTATAGCATTGCTTTTGGTTGAGGGTGGTAGAAC +AGCCCATTCTCGATTTAAAATACCCATAGATGTCAATGAATATAACAATTGTGAAATTAA +ACAGAACATCTACCTCGCTGAACTTATATGTCACACCAATTTGGTCATTTGGGATGAGGC +ACCTATGACTCAATATTTTGTCTTTGAGGCGGTTGA +>contig_10 +GGGGCATTGCCGCCGATTAATTCGAGCGCGAGGTTTCGCGTATCAGGCGGAATTGGGATT +TGGCGCCACAAAGAGCGCCACCTATGATTTCTGTGGCGGACGACTTCACGAACTCGGACG +GGACTATCTAACCAATCTTCCAAGTTCATTGCGACATCAGTATAAGGGCGTGATGAAGGT +TCGCTATCGTCGCTTGAGTTATTGATGGGGCCCAAATTGAGATCGAGGTTCATTGTAGTG +GTGTTCTCTTCTGCCATTTGAGAATTTCACAAGTTCTAACAAACGAAAACGCAAATCTTC +GGGACTAATATGCAGAATTTCCCTAAATAGAAGGGGTTTAAAA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/transcripts.cleaned.nr.pep Fri Dec 09 08:45:36 2016 -0500 @@ -0,0 +1,7 @@ +>contig_2 +LSKVPIPSNNIYAINDKKSPEDAADDYENRLKELVSEKIIPVSTISGFPKFDLMLLGMGPDGHVASLFPSHMQRYEKEKW +VTFITDSPKPPPSRITFTFPMINSASEIAMVVTGADLAGTTKIALGTTGNVKPGETPLPCTEVSAEGEVTWFLDKDAASQ +LLNYVRFDD +>contig_9 +LRLKADEEAQCLNQMQRIIFDEIMEHVELEKGGFYFVYRPGGNGKTLWLAIISKLRSEGRIVLAVASSGIALLLVEGGRT +AHSRFKIPIDVNEYNNCEIKQNIYLAELICHTNLVIWDEAPMTQYFVFEAV
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Fri Dec 09 08:45:36 2016 -0500 @@ -0,0 +1,6 @@ +<tables> + <table name="plant_tribes_scaffolds" comment_char="#"> + <columns>value, name, path, description</columns> + <file path="tool-data/plant_tribes_scaffolds.loc" /> + </table> +</tables>