Mercurial > repos > abims-sbr > pairwise
diff pairwise.xml @ 4:6709645eff5d draft
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
| author | abims-sbr |
|---|---|
| date | Wed, 17 Jan 2018 08:53:53 -0500 |
| parents | 5f68b2fc02c1 |
| children | 6e44f0c3e7c1 |
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--- a/pairwise.xml Wed Sep 27 10:01:55 2017 -0400 +++ b/pairwise.xml Wed Jan 17 08:53:53 2018 -0500 @@ -22,6 +22,7 @@ #end for #set $infiles = $infiles[:-1] + ln -s $__tool_directory__/scripts/functions.py . && ln -s $__tool_directory__/scripts/S02_xxx_patron_pipeline.sh . && ln -s $__tool_directory__/scripts/S03_run_blast_with_k_filter.sh . && ln -s $__tool_directory__/scripts/S04_run_blast2_with_k_filter.sh . && @@ -54,6 +55,16 @@ </outputs> <tests> + <test> + <param name="inputs" ftype="fasta" value="inputs2/PfPfiji_trinity.fasta,inputs2/ApApomp_trinity.fasta,inputs2/AmAmphi_trinity.fasta,inputs2/AcAcaud_trinity.fasta" /> + <param name="e-value" value="1e-5" /> + <output_collection name="output_fasta_dna" type="list"> + <element name="DNAalignment_corresponding_to_protein_from_RBH_AmAmphi_AcAcaud" value="outputs_dna2/DNAalignment_corresponding_to_protein_from_RBH_AmAmphi_AcAcaud.fasta" /> + <element name="DNAalignment_corresponding_to_protein_from_RBH_PfPfiji_AcAcaud" value="outputs_dna2/DNAalignment_corresponding_to_protein_from_RBH_PfPfiji_AcAcaud.fasta" /> + <element name="DNAalignment_corresponding_to_protein_from_RBH_PfPfiji_AmAmphi" value="outputs_dna2/DNAalignment_corresponding_to_protein_from_RBH_PfPfiji_AmAmphi.fasta" /> + <element name="DNAalignment_corresponding_to_protein_from_RBH_PfPfiji_ApApomp" value="outputs_dna2/DNAalignment_corresponding_to_protein_from_RBH_PfPfiji_ApApomp.fasta" /> + </output_collection> + </test> <test> <param name="inputs" ftype="fasta" value="inputs/PfPfiji_Trinity.fasta,inputs/ApApomp_Trinity.fasta,inputs/AmAmphi_Trinity.fasta,inputs/AcAcaud_Trinity.fasta" /> <param name="e-value" value="1e-5" /> @@ -94,185 +105,45 @@ <help> -@HELP_AUTHORS@ - -============ -What it does -============ - -| This tool takes a 'data collection list' containing nucleic fasta sequence files and searches different homologous genes from pairwise comparaisons. -| There are 3 outputs. -| - --------- + @HELPAUTHORS@ + +<![CDATA[ +--------- -========== -Parameters -========== - -The choice of parameters is possible : +**Description** -**-e** : - | is the option for the choice of the e-value. - | By default it's 10. - | - +This tool searches for different homologous genes from pairwise comparisons between a set of fasta files (one file per species). + -------- -======= -Outputs -======= - -This tool, produces the following files : - -**Pairwise**: - | is the general output. It gives the information about what the tool is doing (for each pairwise). - | +**Parameters** -**Pairwise DNA**: - | is the output wich contains nucleic sequences (of the pairwise) that are homologues. The sequences are with nucleotides. Shows: - | the name of the query sequence - | the part of the sequence in nucleotides - | the name of the match sequence - | the part of the sequence in nucleotides - | - -**Pairwise PROT**: - | is the output wich contains proteic sequences (of the pairwise) that are homologues. The sequences are with protein. Shows: - | the name of the query sequence (the name of the sequence || the position (Start and End) of the homologous sequences || divergence || number of gaps || real divergence || the length of the homologous sequence) - | the part of the sequence in protein - | the name of the match sequence (the name of the sequence || the position (Start and End) of the homologous sequences || divergence || number of gaps || real divergence || the length of the homologous sequence) - | the part of the sequence in protein + - 'Input files' : a collection of fasta files (one file per species) + - 'e_value' : the blast e-value. By default it's 1e-5. -------- -=============== -Working Example -=============== - ---------------------------- -The input files and options ---------------------------- +**Outputs** -**Input files** - | 3 files with 200 nucleic sequences each : Ap.fasta, Ac.fasta et Pp.fasta - | -**Parameters** - | e-value = 1e-20 - | - ----------------- -The output files ----------------- - -**Pairwise** + - 'Pairwise' : the general output. It gives the information about what the tool has done for each pairwise. -| -------------------- Pairwise Pp_Ap -------------------- -| -| database : Pp.fasta -| query file : Ap.fasta -| -| ***** START run BLAST ***** -| ***** END run BLAST ***** -| -| -| database : Ap.fasta -| query file : only the sequences of Pp.fasta who matched during the last BLAST -| -| ***** START run BLAST ***** -| ***** END run BLAST ***** -| -| [3/5] Get pairs of sequences ... -| Get list of fasta name involved in RBH -| Number of pairwises parsed = 15 -| Get subset of Alvinella db -| Get subset of Paralvinella db -| -| -------------------- Pairwise Pp_Ac -------------------- -| -| database : Pp.fasta -| query file : Ac.fasta -| -| ***** START run BLAST ***** -| ***** END run BLAST ***** -| -| -| database : Ac.fasta -| query file : only the sequences of Pp.fasta who matched during the last BLAST -| -| ***** START run BLAST ***** -| ***** END run BLAST ***** -| -| [3/5] Get pairs of sequences ... -| Get list of fasta name involved in RBH -| Number of pairwises parsed = 13 -| Get subset of Alvinella db -| Get subset of Paralvinella db -| -| -| -------------------- Pairwise Ap_Ac -------------------- -| -| database : Ap.fasta -| query file : Ac.fasta -| -| ***** START run BLAST ***** -| ***** END run BLAST ***** -| -| -| database : Ac.fasta -| query file : only the sequences of Ap.fasta who matched during the last BLAST -| -| ***** START run BLAST ***** -| ***** END run BLAST ***** -| -| [3/5] Get pairs of sequences ... -| Get list of fasta name involved in RBH -| Number of pairwises parsed = 24 -| Get subset of Alvinella db -| Get subset of Paralvinella db -| -| + - 'Pairwise_DNA' : the output which contains nucleic sequences (of the pairwise) that are homologous. The sequences are with nucleotides. It shows for both the query and match : + the name + the sequence in nucleotides + + - 'Pairwise_PROT' : the output which contains proteic sequences (of the pairwise) that are homologous. The sequences are with protein. It shows : + Name, position, length, and part of the sequence in protein for query and match sequences + Divergence + Number of gaps + Real divergence -**Pairwise_output_file_PROT** +-------- -| For example the 4 last sequences of the file 19_ReciprocalBestHits_Pp_Ap.fasta -| -| >Ap123_1/1_1.000_748||254...478||[[1/1]][[1/6]]||29.3333333333||0||29.3333333333||75.0 -| FVRITVGDEMSRRPKFAMITWVGPEVSPMKRAKVSTDKAFVKQIFQNFAKEIQTSERSELEEEYVRQEVMKAGGA -| >Pp_146_1/2_1.000_713||259...483||[[1/1]][[1/6]]||29.3333333333||0||29.3333333333||75.0 -| FAYIRCTNEESKRSKFAMITWIGQGVEAMKRAKVSMDKQFLKEIFQNFAREFQTSEKSELDEVCIKHALAIDDGA -| >Ap66_1/1_1.000_400||192...398||[[1/1]][[1/6]]||21.7391304348||0||21.7391304348||69.0 -| LSTSLLNWRKHTLCF*GMKLILIILLISFIIPAILFLLSIFTTMRMPESREKFRPYECGFDPNHSARTP -| >Pp_201_2/2_1.000_691||14...220||[[1/1]][[1/6]]||21.7391304348||0||21.7391304348||69.0 -| LSTSLLN*RKQPFASEEMKLLILLLFISALIPRILIILSIFTSIRTPKNREKSSPYECGFDPNHSARTP -| -| - -**Pairwise_output_file_DNA** +**The AdaptSearch Pipeline** -| For example the 4 last sequences of the file 25_DNAalignement_corresponding_to_protein_from_19_RBH_Pp_Ap.fasta -| -| >Ap123_1/1_1.000_748 -| CCAGTAACAAGCCGCCACGGGTCCGTCGTGTCTTCTCTTCAAGGAAAGGTTGACAGATTCTCGTACGCTAGACGTCGCCACCTACTCGTCCTGGACTCCGGTGCCGTAGGTGGCGCCACCTGCTTTCATCACTTCCTGCCTA -| ACGTACTCCTCTTCTAGCTCCGATCTCTCGCTCGTCTGGATCTCTTTGGCAAAGTTCTGGAATATCTGCTTGACGAACGCCTTGTCCGTGCTGACTTTGGCGCGCTTCATTGGGCTCACTTCCGGTCCGACCCACGTGATCA -| TGGCGAACTTCGGTCTTCTGCTCATTTCGTCCCCGACGGTAATACGGACAAAGGCGAACGCCCGCTGGTCATCTTGTAGTTTTGATAACAGATCCTCGTATTCGGTTCCTGTAGAGTCCAGTATAATATTGTCGCCATCATA -| CGTCACAAACGCCCAGTTTGTCTCCGTCGCGTCGCTCCTGACGTCTTCGTAAGCCTGTCCGATAGCCTCTCTGTCGATGTCTGCCATGCTGCTGGTCCCGCTCTCGACGCTAATGAGCCAATCACGACTTCTGACAGACGAG -| TAGACATGCAGACAGCCAGACGGACTGACGGACTGACG -| >Pp_146_1/2_1.000_713 -| CATTAATTGTGTGTCTGGTTGTGGGTGTGTGTTATAAGAGACATCACTTAGTGTATACTGATGTCCACGTGGTAGTTGACCAGCATGTCGAATATGGATAGGGACTCGATCTTGAATGGCTATGAGGAGGTTCGCAACGACGA -| CTCGGACATTAACTGGGCTTTCGTAACGTATTCACCTGACAACAAACTAGTACTTGATTCAACTGGCACAGACTACTTCCAGCTCCAGGAGAAATATCAAGATGATATGCGAGGATTTGCTTACATCCGGTGCACTAACGAGG -| AGAGTAAACGTTCTAAATTTGCCATGATTACCTGGATTGGACAAGGAGTGGAAGCAATGAAGCGTGCCAAGGTCAGCATGGACAAACAGTTCCTAAAGGAAATCTTCCAGAATTTCGCAAGAGAATTTCAGACGAGTGAAAAG -| TCAGAGCTTGATGAGGTCTGTATTAAACACGCGCTTGCCATTGACGATGGAGCTGGTTGCAAAGTGGAAAGCGAGGACACGAGAAAAGGGGCCTTTCTCAGGAAAGAGGATGACACTGAAGTGGAAAGGGAAACTAATGTCAA -| CAATGTCTCCGGTGTCGTGGAAGAAGATGATGACGCAAAAAATGCAAATGATTTTAATTACGAAGAGGACTGTAACAATGAATAGGTGCATGTCGATGATTTATATAGAGAACTAGACTTCGCACTCGCTAGGTGGTTGAT -| >Ap66_1/1_1.000_400 -| TGATCGTCTTATAAACCTAACTTGAAAAACCTTCCTACCATTTAGGGCTAGCAGCCCTATTAATTATCACACCTATCGCAGCGCTCTCACTATAATTATAAGTATTGCGCCGGGTTTGAACGGATAGCTCTGATGCTGCTAATT -| ACGGGACCTAATAATCCCCAATACTTTATCCTTAGAGAGCTGTACCTCTTAGCACCAGTCTTTTAAACTGGCGAAAGCACACTTTATGCTTCTAAGGAATGAAACTAATTCTTATAATCCTACTAATCTCTTTTATCATCCCCG -| CCATTCTATTTTTACTCTCGATCTTTACTACTATGCGCATGCCAGAGAGCCGTGAAAAATTTAGGCCCTACGAGTGCGGGTTTGACCCCAATCACTCGGCCCGAACCCCATT -| >Pp_201_2/2_1.000_691 -| ATCGTAGGGAAAAAGGTGTTCGTGCAGAATGATTGGGGTCAAATCCACATTCGTAGGGGCTAGATTTTTCACGGTTTTTAGGTGTACGAATAGAGGTGAAGATTGATAGGATGATTAAAATTCTTGGGATTAATGCTGAAATAAA -| GAGAAGTAGGATTAAAAGTTTCATTTCCTCAGAAGCAAAGGGTTGCTTTCGTCAGTTTAAAAGACTGGTGCTAAGTAGGTACAGCTCTCTAAGGG +.. image:: ../../adaptsearch_picture_helps.png :heigth: 593 :width: 852 ---------------------------------------------------- +--------- Changelog --------- @@ -284,10 +155,11 @@ **Version 1.0 - 13/04/2017** - - TEST: Add funtional test with planemo + - TEST: Add functional test with planemo - IMPROVEMENT: Use conda dependencies for blast, samtools and python + ]]> </help> <expand macro="citations" />