Mercurial > repos > abims-sbr > pairwise
diff pairwise.xml @ 3:5f68b2fc02c1 draft
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
| author | abims-sbr |
|---|---|
| date | Wed, 27 Sep 2017 10:01:55 -0400 |
| parents | e95d4b20c62d |
| children | 6709645eff5d |
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--- a/pairwise.xml Mon May 29 04:06:55 2017 -0400 +++ b/pairwise.xml Wed Sep 27 10:01:55 2017 -0400 @@ -1,6 +1,4 @@ -<?xml version="1.0"?> - -<tool name="Pairwise" id="pairwise" version="1.0"> +<tool name="Pairwise" id="pairwise" version="2.0"> <description> Run reciproque tblastx pairwise @@ -11,56 +9,53 @@ </macros> <requirements> - <expand macro="python_required" /> - <requirement type="package" version="2.2.22">blast-legacy</requirement> + <expand macro="python_required" /> + <requirement type="package" version="2.2.22">blast-legacy</requirement> <requirement type="package" version="1.3.1">samtools</requirement> </requirements> - <command> - <![CDATA[ - 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 . - && - ln -s $__tool_directory__/scripts/S05_script_extract_match_v20_blastx.py . - && - ln -s $__tool_directory__/scripts/S06_post_processing_of_pairwise.py . - && - ln -s $__tool_directory__/scripts/S07_format_match_get_back_nucleotides.py . - && - ln -s $__tool_directory__/scripts/S08_script_extract_match_v20_blastx.py . - && - ln -s $__tool_directory__/scripts/S09_post_processing_of_pairwise.py . - && - ln -s $__tool_directory__/scripts/S10_compare_list_pairs_for_reciprocal_best_hits_test.py . - && - ln -s $__tool_directory__/scripts/S11_post_processing_of_pairwise.py . - && - ln -s $__tool_directory__/scripts/S12_prot2dna.py . - && - ln -s $__tool_directory__/scripts/S13_zip.py . - && - python $__tool_directory__/scripts/S01_organize_rbh.py 8 ${e_value} ${zip} + <command><![CDATA[ + #set $infiles = "" + #for $input in $inputs + ln -s '$input' '$input.element_identifier'; + #set $infiles = $infiles + $input.element_identifier + "," + #end for + #set $infiles = $infiles[:-1] + + 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 . && + ln -s $__tool_directory__/scripts/S05_script_extract_match_v20_blastx.py . && + ln -s $__tool_directory__/scripts/S06_post_processing_of_pairwise.py . && + ln -s $__tool_directory__/scripts/S07_format_match_get_back_nucleotides.py . && + ln -s $__tool_directory__/scripts/S08_script_extract_match_v20_blastx.py . && + ln -s $__tool_directory__/scripts/S09_post_processing_of_pairwise.py . && + ln -s $__tool_directory__/scripts/S10_compare_list_pairs_for_reciprocal_best_hits_test.py . && + ln -s $__tool_directory__/scripts/S11_post_processing_of_pairwise.py . && + ln -s $__tool_directory__/scripts/S12_prot2dna.py . && + + python $__tool_directory__/scripts/S01_organize_rbh.py $infiles ${e_value} \${GALAXY_SLOTS:-1} > ${output}; - ]]> - </command> + ]]></command> <inputs> - <param name="zip" type="data" format="no_unzip.zip,zip" multiple="true" label="Choose your ZIP file" help="Contains the output of the filter tool" /> - <param name="e_value" type="float" value="1e-5" label="e_value" help="By default, it's 1e-5. you can write the e-value like this: 1e-5" /> + <param name="inputs" type="data" format="fasta" multiple="true" label="Input files" /> + <param name="e_value" type="float" value="1e-5" label="e_value" help="By default, it's 1e-5. you can write the e-value like this: 1e-5" /> </inputs> <outputs> <data format="txt" name="output" label="Pairwise" /> - <data format="no_unzip.zip" name="output_zip_DNA" label="Pairwise_zip_DNA" from_work_dir="output_file_DNA.zip" /> - <data format="no_unzip.zip" name="output_zip_PROT" label="Pairwise_zip_PROT" from_work_dir="output_file_PROT.zip" /> + <collection name="output_fasta_dna" type="list" label="Pairwise DNA"> + <discover_datasets pattern="__name_and_ext__" directory="outputs_dna" /> + </collection> + <collection name="output_fasta_prot" type="list" label="Pairwise PROT"> + <discover_datasets pattern="__name_and_ext__" directory="outputs_prot" /> + </collection> </outputs> <tests> <test> - <param name="zip" ftype="zip" value="test_02_input_pairwise.zip" /> + <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" /> <output name="output" > <assert_contents> @@ -70,30 +65,44 @@ <has_line line="('ApApomp_Trinity.fasta', 'AmAmphi_Trinity.fasta')"/> <has_line line="('ApApomp_Trinity.fasta', 'AcAcaud_Trinity.fasta')"/> <has_line line="('AmAmphi_Trinity.fasta', 'AcAcaud_Trinity.fasta')"/> - + <has_text text="Number of pairwises parsed = 2" /> <has_text text="Number of pairwises parsed = 3" /> <has_text text="Number of pairwises parsed = 0" /> - <has_text text="Number of pairwises parsed = 5" /> + <has_text text="Number of pairwises parsed = 5" /> <has_text text="Number of pairwises parsed = 1" /> - </assert_contents> </output> + <output_collection name="output_fasta_prot" type="list"> + <element name="ReciprocalBestHits_AmAmphi_AcAcaud" value="outputs_prot/ReciprocalBestHits_AmAmphi_AcAcaud.fasta" /> + <element name="ReciprocalBestHits_ApApomp_AcAcaud" value="outputs_prot/ReciprocalBestHits_ApApomp_AcAcaud.fasta" /> + <element name="ReciprocalBestHits_ApApomp_AmAmphi" value="outputs_prot/ReciprocalBestHits_ApApomp_AmAmphi.fasta" /> + <element name="ReciprocalBestHits_PfPfiji_AcAcaud" value="outputs_prot/ReciprocalBestHits_PfPfiji_AcAcaud.fasta" /> + <element name="ReciprocalBestHits_PfPfiji_AmAmphi" value="outputs_prot/ReciprocalBestHits_PfPfiji_AmAmphi.fasta" /> + <element name="ReciprocalBestHits_PfPfiji_ApApomp" value="outputs_prot/ReciprocalBestHits_PfPfiji_ApApomp.fasta" /> + </output_collection> + <output_collection name="output_fasta_dna" type="list"> + <element name="DNAalignment_corresponding_to_protein_from_RBH_AmAmphi_AcAcaud" value="outputs_dna/DNAalignment_corresponding_to_protein_from_RBH_AmAmphi_AcAcaud.fasta" /> + <element name="DNAalignment_corresponding_to_protein_from_RBH_ApApomp_AcAcaud" value="outputs_dna/DNAalignment_corresponding_to_protein_from_RBH_ApApomp_AcAcaud.fasta" /> + <element name="DNAalignment_corresponding_to_protein_from_RBH_ApApomp_AmAmphi" value="outputs_dna/DNAalignment_corresponding_to_protein_from_RBH_ApApomp_AmAmphi.fasta" /> + <element name="DNAalignment_corresponding_to_protein_from_RBH_PfPfiji_AcAcaud" value="outputs_dna/DNAalignment_corresponding_to_protein_from_RBH_PfPfiji_AcAcaud.fasta" /> + <element name="DNAalignment_corresponding_to_protein_from_RBH_PfPfiji_AmAmphi" value="outputs_dna/DNAalignment_corresponding_to_protein_from_RBH_PfPfiji_AmAmphi.fasta" /> + <element name="DNAalignment_corresponding_to_protein_from_RBH_PfPfiji_ApApomp" value="outputs_dna/DNAalignment_corresponding_to_protein_from_RBH_PfPfiji_ApApomp.fasta" /> + </output_collection> </test> - </tests> + </tests> <help> +@HELP_AUTHORS@ + ============ What it does ============ -| This tool takes a zip archive containing nucleic fasta sequence files and searches different homologous genes from pairwise comparaisons. +| This tool takes a 'data collection list' containing nucleic fasta sequence files and searches different homologous genes from pairwise comparaisons. | There are 3 outputs. | -| The run blast was written by the **NCBI**. -| The script was written by **Eric Fontanillas**. -| The wrapper was written by **Julie Baffard**. -------- @@ -101,12 +110,12 @@ Parameters ========== -The choice of parameters is possible : +The choice of parameters is possible : **-e** : - | is the option for the choice of the e-value. + | is the option for the choice of the e-value. | By default it's 10. - | + | -------- @@ -116,29 +125,25 @@ This tool, produces the following files : -**Pairwise** : +**Pairwise**: | is the general output. It gives the information about what the tool is doing (for each pairwise). - | + | -**Pairwise_zip_DNA.zip** : - | is the output wich contains nucleic sequences (of the pairwise) that are homologues. The sequences are with nucleotides. Shows : +**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_zip_PROT.zip** : - | is the output wich contains proteic sequences (of the pairwise) that are homologues. The sequences are with protein. Shows : +**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 -.. class:: warningmark - -The two zip outputs have to be downloaded (and extracts the files with a file archiver software), you cannot visualize them with the "eye icon" through the interface. - -------- =============== @@ -151,10 +156,10 @@ **Input files** | 3 files with 200 nucleic sequences each : Ap.fasta, Ac.fasta et Pp.fasta - | + | **Parameters** | e-value = 1e-20 - | + | ---------------- The output files @@ -163,77 +168,75 @@ **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 -| +| 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 -| -| +| 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 -| -| +| Get subset of Paralvinella db +| +| **Pairwise_output_file_PROT** -| Save as *Galaxy{number}-[Pairwise_output_file_PROT].zip* -| If you unzip the file, a number of file appears (number of pairwise) : 19_ReciprocalBestHits_{name_of_pairwise}.fasta | 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 @@ -242,27 +245,25 @@ | 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** - -| Save as *Galaxy{number}-[Pairwise_output_file_DNA].zip* -| If you unzip the file, a number of file appears (number of pairwise) : 25_DNAalignment_corresponding_to_protein_from_19_RBH_{name_of_pairwise}.fasta + | 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 +| >Pp_146_1/2_1.000_713 | CATTAATTGTGTGTCTGGTTGTGGGTGTGTGTTATAAGAGACATCACTTAGTGTATACTGATGTCCACGTGGTAGTTGACCAGCATGTCGAATATGGATAGGGACTCGATCTTGAATGGCTATGAGGAGGTTCGCAACGACGA | CTCGGACATTAACTGGGCTTTCGTAACGTATTCACCTGACAACAAACTAGTACTTGATTCAACTGGCACAGACTACTTCCAGCTCCAGGAGAAATATCAAGATGATATGCGAGGATTTGCTTACATCCGGTGCACTAACGAGG | AGAGTAAACGTTCTAAATTTGCCATGATTACCTGGATTGGACAAGGAGTGGAAGCAATGAAGCGTGCCAAGGTCAGCATGGACAAACAGTTCCTAAAGGAAATCTTCCAGAATTTCGCAAGAGAATTTCAGACGAGTGAAAAG | TCAGAGCTTGATGAGGTCTGTATTAAACACGCGCTTGCCATTGACGATGGAGCTGGTTGCAAAGTGGAAAGCGAGGACACGAGAAAAGGGGCCTTTCTCAGGAAAGAGGATGACACTGAAGTGGAAAGGGAAACTAATGTCAA -| CAATGTCTCCGGTGTCGTGGAAGAAGATGATGACGCAAAAAATGCAAATGATTTTAATTACGAAGAGGACTGTAACAATGAATAGGTGCATGTCGATGATTTATATAGAGAACTAGACTTCGCACTCGCTAGGTGGTTGAT +| CAATGTCTCCGGTGTCGTGGAAGAAGATGATGACGCAAAAAATGCAAATGATTTTAATTACGAAGAGGACTGTAACAATGAATAGGTGCATGTCGATGATTTATATAGAGAACTAGACTTCGCACTCGCTAGGTGGTTGAT | >Ap66_1/1_1.000_400 | TGATCGTCTTATAAACCTAACTTGAAAAACCTTCCTACCATTTAGGGCTAGCAGCCCTATTAATTATCACACCTATCGCAGCGCTCTCACTATAATTATAAGTATTGCGCCGGGTTTGAACGGATAGCTCTGATGCTGCTAATT | ACGGGACCTAATAATCCCCAATACTTTATCCTTAGAGAGCTGTACCTCTTAGCACCAGTCTTTTAAACTGGCGAAAGCACACTTTATGCTTCTAAGGAATGAAACTAATTCTTATAATCCTACTAATCTCTTTTATCATCCCCG @@ -271,6 +272,22 @@ | ATCGTAGGGAAAAAGGTGTTCGTGCAGAATGATTGGGGTCAAATCCACATTCGTAGGGGCTAGATTTTTCACGGTTTTTAGGTGTACGAATAGAGGTGAAGATTGATAGGATGATTAAAATTCTTGGGATTAATGCTGAAATAAA | GAGAAGTAGGATTAAAAGTTTCATTTCCTCAGAAGCAAAGGGTTGCTTTCGTCAGTTTAAAAGACTGGTGCTAAGTAGGTACAGCTCTCTAAGGG +--------------------------------------------------- + +Changelog +--------- + +**Version 2.0 - 18/04/2017** + + - NEW: Replace the zip between tools by Dataset Collection + + +**Version 1.0 - 13/04/2017** + + - TEST: Add funtional test with planemo + + - IMPROVEMENT: Use conda dependencies for blast, samtools and python + </help> <expand macro="citations" />