proteinortho: proteinortho.xml annotate

annotate proteinortho.xml @ 6:10112d9127af draft

planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit ebbb4da7c0c0176df539f9baa7c9323d9ff5f201

author	iuc
date	Tue, 31 Oct 2023 16:32:03 +0000
parents	5532c0e5d4a6
children	c5dd4f86d981

rev	line source
1 26abc7846e6f "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5" iuc parents: 0 diff changeset	1 <tool id="proteinortho" name="Proteinortho" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@" profile="@PROFILE@">
0 4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	2 <description>detects orthologous proteins/genes within different species</description>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	3 <macros>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	4 <import>proteinortho_macros.xml</import>
5 5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	5 <xml name="test_output_proteinortho" tokens="nlines">
1 26abc7846e6f "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5" iuc parents: 0 diff changeset	6 <output name="proteinortho">
5 5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	7 <metadata name="column_names" value="species,genes,alg.-conn.,L.fasta,C.fasta,E.fasta,M.fasta"/>
1 26abc7846e6f "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5" iuc parents: 0 diff changeset	8 <assert_contents>
5 5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	9 <has_n_columns n="7"/>
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	10 <has_n_lines n="@NLINES@"/>
1 26abc7846e6f "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5" iuc parents: 0 diff changeset	11 <has_line_matching expression="# Species\tGenes\tAlg\.-Conn\.\t.*"/>
26abc7846e6f "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5" iuc parents: 0 diff changeset	12 <has_line_matching expression="[0-9]+\t[0-9]+\t.*"/>
26abc7846e6f "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5" iuc parents: 0 diff changeset	13 <has_line_matching expression=".(C\|C2\|E\|L\|M)_[0-9]+."/>
26abc7846e6f "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5" iuc parents: 0 diff changeset	14 </assert_contents>
26abc7846e6f "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5" iuc parents: 0 diff changeset	15 </output>
5 5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	16 </xml>
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	17 <xml name="test_output_blastgraph" tokens="nlines">
1 26abc7846e6f "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5" iuc parents: 0 diff changeset	18 <output name="blastgraph">
5 5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	19 <metadata name="column_names" value="seqidA,seqidB,evalue_ab,bitscore_ab,evalue_ba,bitscore_ba"/>
1 26abc7846e6f "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5" iuc parents: 0 diff changeset	20 <assert_contents>
5 5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	21 <has_n_columns n="6" comment="#"/>
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	22 <has_n_lines n="@NLINES@"/>
1 26abc7846e6f "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5" iuc parents: 0 diff changeset	23 <has_line_matching expression="# file_a\tfile_b"/>
26abc7846e6f "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5" iuc parents: 0 diff changeset	24 <has_line_matching expression="# a\tb\tevalue_ab\tbitscore_ab\tevalue_ba\tbitscore_ba"/>
26abc7846e6f "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5" iuc parents: 0 diff changeset	25 <has_line_matching expression="# (C\|C2\|E\|L\|M)\.fasta\t(C\|C2\|E\|L\|M)\.fasta"/>
26abc7846e6f "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5" iuc parents: 0 diff changeset	26 <has_line_matching expression=".(C\|C2\|E\|L\|M)_[0-9]+\t(C\|C2\|E\|L\|M)_[0-9]+."/>
26abc7846e6f "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5" iuc parents: 0 diff changeset	27 </assert_contents>
26abc7846e6f "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5" iuc parents: 0 diff changeset	28 </output>
5 5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	29 </xml>
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	30 <xml name="test_output_proteinorthograph" tokens="nlines" token_nlines_delta="0" token_add_columns="" token_ncolumns="6">
1 26abc7846e6f "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5" iuc parents: 0 diff changeset	31 <output name="proteinorthograph">
5 5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	32 <metadata name="column_names" value="seqidA,seqidB,evalue_ab,bitscore_ab,evalue_ba,bitscore_ba@ADD_COLUMNS@"/>
1 26abc7846e6f "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5" iuc parents: 0 diff changeset	33 <assert_contents>
5 5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	34 <has_n_columns n="@NCOLUMNS@" comment="#"/>
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	35 <has_n_lines n="@NLINES@" delta="@NLINES_DELTA@"/>
1 26abc7846e6f "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5" iuc parents: 0 diff changeset	36 <has_line_matching expression="# file_a\tfile_b"/>
26abc7846e6f "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5" iuc parents: 0 diff changeset	37 <has_line_matching expression="# a\tb\tevalue_ab\tbitscore_ab\tevalue_ba\tbitscore_ba(\tsame_strand\tsimscore)?"/>
26abc7846e6f "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5" iuc parents: 0 diff changeset	38 <has_line_matching expression="# (C\|C2\|E\|L\|M)\.fasta\t(C\|C2\|E\|L\|M)\.fasta"/>
26abc7846e6f "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5" iuc parents: 0 diff changeset	39 <has_line_matching expression=".(C\|C2\|E\|L\|M)_[0-9]+\t(C\|C2\|E\|L\|M)_[0-9]+."/>
26abc7846e6f "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5" iuc parents: 0 diff changeset	40 </assert_contents>
26abc7846e6f "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5" iuc parents: 0 diff changeset	41 </output>
26abc7846e6f "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5" iuc parents: 0 diff changeset	42 </xml>
0 4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	43 </macros>
6 10112d9127af planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit ebbb4da7c0c0176df539f9baa7c9323d9ff5f201 iuc parents: 5 diff changeset	44 <expand macro="biotools"/>
0 4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	45 <expand macro="requirements"/>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	46 <expand macro="version_command"/>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	47 <command detect_errors="exit_code"><![CDATA[
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	48 ## the following ln-action is necessary, since the file names are used by proteinortho (output contains filenames => species names)
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	49 #import re
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	50 #for $f in $input_files#
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	51 ln -sf '$f' '${re.sub('[^\w\-_.]', '_', f.element_identifier)}' &&
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	52 #end for
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	53 #if $synteny.synteny_options == "specified":
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	54 #for $f in $synteny.input_files_syn#
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	55 ln -sf '$f' '${re.sub('[^\w\-_.]', '_', f.element_identifier)}' &&
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	56 #end for#
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	57 #end if
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	58 proteinortho
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	59 --project=result
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	60 --cpus="\${GALAXY_SLOTS:-4}"
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	61 #if $more_options.selfblast:
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	62 $more_options.selfblast
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	63 #end if
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	64 #if $more_options.singles:
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	65 $more_options.singles
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	66 #end if
5 5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	67 #if $more_options.core:
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	68 $more_options.core
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	69 #end if
0 4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	70 --p=$p
5 5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	71 --e=$more_options.evalue
2 a8addd4fb60a "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit e3b372fc401662aa541a893024c65aa645f5e8cf" iuc parents: 1 diff changeset	72 --conn=$conn
0 4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	73 #if $more_options.cov:
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	74 --cov=$more_options.cov
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	75 #end if
5 5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	76 #if $sim:
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	77 --sim=`LC_NUMERIC=C awk "BEGIN {printf \"%.2f\",$sim/100}"`
0 4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	78 #end if
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	79 #if $more_options.identity:
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	80 --cov=$more_options.identity
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	81 #end if
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	82 #if $more_options.isoform != "no":
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	83 --isoform=$more_options.isoform
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	84 #end if
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	85 #if $synteny.synteny_options == "specified":
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	86 --synteny
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	87 --dups=$synteny.dups
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	88 --cs=$synteny.cs
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	89 --alpha=$synteny.alpha
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	90 #end if
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	91 #for $f in $input_files#
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	92 ${re.sub('[^\w\-_.]', '_', f.element_identifier)}
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	93 #end for#
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	94 #if $synteny.synteny_options == "specified":
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	95 #for $f in $synteny.input_files_syn#
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	96 ${re.sub('[^\w\-_.]', '_', f.element_identifier)}
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	97 #end for#
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	98 #end if
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	99 2> >(sed -E "s/.\[([0-9]{1,2}(;[0-9]{1,2})?)?[mGK]//g" 1>&2)
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	100 #if $synteny.synteny_options == "specified":
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	101 &&
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	102 mv result.poff-graph result.proteinortho-graph &&
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	103 mv result.poff.tsv result.proteinortho.tsv &&
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	104 mv result.poff.html result.proteinortho.html ;
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	105 #end if
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	106 ]]></command>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	107 <inputs>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	108 <param name="input_files" format="fasta" type="data" multiple="true" min="2" label="Select the input fasta files (>2)" help="The input fasta files. At least 2 are needed!"/>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	109 <param argument="--p" type="select" label="Similarity comparision algorithm" help="In the first step of proteinortho an all-versus-all reciprocal best hit graph is build from the input files (using this algorithm).">
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	110 <option value="diamond" selected="true">diamond (aminoacid sequences)</option>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	111 <option value="autoblast">auto detect NCBI-BLAST (protein and nucleotide sequences)</option>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	112 <option value="blastp">NCBI-BLASTP+ (protein sequences)</option>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	113 <option value="blastn">NCBI-BLASTN+ (nucleotide sequences)</option>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	114 <option value="lastp">Last (aminoacid sequences)</option>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	115 <option value="lastn">Last (nucleotide sequences)</option>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	116 <option value="blatp">BLAT (aminoacid sequences)</option>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	117 <option value="blatn">BLAT (nucleotide sequences)</option>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	118 </param>
5 5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	119 <param argument="--sim" type="integer" value="95" min="0" max="100" label="Minimal reciprocal similarity in %" help="This and --evalue are main parameters for the generation of the reciprocal best hit graph. 1 = only the best reciprocal hits are reported, 0 = all possible reciprocal blast matches (within the E-value cutoff) are reported."/>
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	120 <param argument="--conn" type="float" value="0.1" min="0." max="1." label="Minimal algebraic connectivity" help="This is the main parameter for the clustering step. Choose larger values than more splits are done, resulting in more and smaller clusters. A value of 0 corresponds to no clustering."/>
0 4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	121 <section name="more_options" title="Additional Options" expanded="False">
5 5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	122 <param argument="--evalue" type="float" value="0.001" min="0" label="E-value threshold of the blast algorithm" help="Larger values results in more false positives (connections between proteins)."/>
0 4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	123 <param argument="--cov" type="integer" value="50" min="0" max="100" label="Minimal coverage of best blast alignments in %"/>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	124 <param argument="--identity" type="integer" value="25" min="0" max="100" label="Minimal percent identity of best blast hits in %"/>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	125 <param argument="--selfblast" type="boolean" checked="false" truevalue="--selfblast" falsevalue="" label="Apply selfblast, detects paralogs without orthologs "/>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	126 <param argument="--singles" type="boolean" checked="false" truevalue="--singles" falsevalue="" label="Report singleton genes without any hit "/>
5 5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	127 <param argument="--core" type="boolean" checked="false" truevalue="--core" falsevalue="" label="Stop clustering if a split would result in groups that do not span across all species of the inital connected component." help="Overrules the -conn threshold."/>
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	128 <param argument="--isoform" type="select" label="Use isoform information" help="The reciprocal best hit graph is built using isoform information (isoforms are treated equivalent). For ncbi : simply add the additional files to the input (file names need to match). For Uniprot : the isoforms need to contain the word isoform and the corresponding identifier. For trinity simply use the trinity output format.">
0 4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	129 <option value="no" selected="true">Don't use isoform information</option>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	130 <option value="ncbi">ncbi style (..._additional.fasta)</option>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	131 <option value="uniprot">uniprot style (...isoform of...)</option>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	132 <option value="trinity">trinity style (...i4)</option>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	133 </param>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	134 </section>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	135 <conditional name="synteny">
5 5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	136 <param name="synteny_options" type="select" label="Activate synteny feature (POFF)" help="To enhance the prediction accuracy, the relative order of genes (synteny) can be used as an additional feature for the discrimination of orthologs. For more details see doi:10.1371/journal.pone.0105015.">
0 4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	137 <option value="no" selected="true">no</option>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	138 <option value="specified">yes</option>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	139 </param>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	140 <when value="no"/>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	141 <when value="specified">
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	142 <param argument="--dups" type="integer" value="0" min="0" max="100" label="Number of reiterations for adjacencies heuristic, to determine duplicated regions"/>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	143 <param argument="--cs" type="integer" value="3" min="0" max="100" label="Size of a maximum common substring (MCS) for adjacency matches"/>
5 5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	144 <param argument="--alpha" type="float" value="0.5" min="0." max="1." label="Weight of adjacencies vs. sequence similarity" help="alpha[FF-adj score] + (1−alpha)[BLAST score]"/>
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	145 <param name="input_files_syn" type="data" format="gff" multiple="true" min="2" label="Select the GFF3 files matching the input fasta files" help="The GFF3 files need matching names with the input fasta files. If you provide mybacteria123.faa or mybacteria123.fasta ... then you need to provide mybacteria123.gff here accordingly. The attributes column (#9) must contain the attribute Name=GENE IDENTIFIER where GENE IDENTIFIER corresponds to the respective (protein) identifier in the FASTA input. For example see https://gitlab.com/paulklemm_PHD/proteinortho/-/blob/master/test/C.gff"/>
0 4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	146 </when>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	147 </conditional>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	148 </inputs>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	149 <outputs>
5 5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	150 <data name="blastgraph" format="tabular" label="${tool.name} on ${on_string}: RBH graph" from_work_dir="result.blast-graph">
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	151 <actions>
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	152 <action name="column_names" type="metadata"
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	153 default="seqidA,seqidB,evalue_ab,bitscore_ab,evalue_ba,bitscore_ba"/>
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	154 </actions>
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	155 </data>
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	156 <data name="proteinortho" format="tabular" label="${tool.name} on ${on_string}: orthology-groups" from_work_dir="result.proteinortho.tsv">
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	157 <actions>
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	158 <action name="column_names" type="metadata"
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	159 default="species,genes,alg.-conn.,${','.join([ f.element_identifier for f in $input_files ])}"/>
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	160 </actions>
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	161 </data>
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	162 <data name="proteinorthograph" format="tabular" label="${tool.name} on ${on_string}: orthology-pairs" from_work_dir="result.proteinortho-graph">
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	163 <actions>
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	164 <conditional name="synteny.synteny_options">
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	165 <when value="no">
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	166 <action name="column_names" type="metadata" default="seqidA,seqidB,evalue_ab,bitscore_ab,evalue_ba,bitscore_ba"/>
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	167 </when>
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	168 <when value="specified">
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	169 <action name="column_names" type="metadata" default="seqidA,seqidB,evalue_ab,bitscore_ab,evalue_ba,bitscore_ba,same_strand,simscore"/>
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	170 </when>
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	171 </conditional>
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	172 </actions>
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	173 </data>
0 4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	174 </outputs>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	175 <tests>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	176 <test expect_num_outputs="3"> <!-- test normal -->
5 5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	177 <param name="input_files" value="L.fasta,C.fasta,E.fasta,M.fasta"/>
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	178 <param name="p" value="diamond"/>
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	179 <expand macro="test_output_proteinortho" nlines="34"/>
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	180 <expand macro="test_output_blastgraph" nlines="157"/>
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	181 <expand macro="test_output_proteinorthograph" nlines="134"/>
1 26abc7846e6f "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5" iuc parents: 0 diff changeset	182 <assert_command>
26abc7846e6f "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5" iuc parents: 0 diff changeset	183 <has_text text="--p=diamond"/>
26abc7846e6f "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5" iuc parents: 0 diff changeset	184 </assert_command>
0 4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	185 </test>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	186 <test expect_num_outputs="3"> <!-- various parameter -->
5 5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	187 <param name="input_files" value="L.fasta,C.fasta,E.fasta,M.fasta"/>
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	188 <param name="p" value="diamond"/>
0 4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	189 <param name="conn" value="1"/>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	190 <param name="sim" value="42"/>
5 5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	191 <section name="more_options">
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	192 <param name="cov" value="42"/>
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	193 <param name="identity" value="42"/>
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	194 <param name="selfblast" value="true"/>
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	195 <param name="singles" value="true"/>
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	196 <param name="core" value="true"/>
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	197 </section>
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	198 <expand macro="test_output_proteinortho" nlines="177"/>
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	199 <expand macro="test_output_blastgraph" nlines="2720"/>
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	200 <expand macro="test_output_proteinorthograph" nlines="384"/>
1 26abc7846e6f "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5" iuc parents: 0 diff changeset	201 <assert_command>
26abc7846e6f "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5" iuc parents: 0 diff changeset	202 <has_text text="--p=diamond"/>
26abc7846e6f "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5" iuc parents: 0 diff changeset	203 </assert_command>
0 4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	204 </test>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	205 <test expect_num_outputs="3"> <!-- synteny -->
5 5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	206 <param name="input_files" value="L.fasta,C.fasta,E.fasta,M.fasta"/>
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	207 <param name="input_files_syn" value="L.gff,C.gff,E.gff,M.gff"/>
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	208 <param name="p" value="diamond"/>
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	209 <conditional name="synteny">
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	210 <param name="synteny_options" value="specified"/>
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	211 </conditional>
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	212 <expand macro="test_output_proteinortho" nlines="38"/>
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	213 <expand macro="test_output_blastgraph" nlines="157"/>
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	214 <expand macro="test_output_proteinorthograph" nlines="119" nlines_delta="10" ncolumns="8" add_columns=",same_strand,simscore"/>
1 26abc7846e6f "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5" iuc parents: 0 diff changeset	215 <assert_command>
26abc7846e6f "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5" iuc parents: 0 diff changeset	216 <has_text text="--p=diamond"/>
26abc7846e6f "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5" iuc parents: 0 diff changeset	217 </assert_command>
0 4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	218 </test>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	219 <test expect_num_outputs="3"> <!-- blast -->
5 5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	220 <param name="input_files" value="L.fasta,C.fasta,E.fasta,M.fasta"/>
1 26abc7846e6f "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5" iuc parents: 0 diff changeset	221 <param name="p" value="blastp"/>
5 5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	222 <expand macro="test_output_proteinortho" nlines="32"/>
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	223 <expand macro="test_output_blastgraph" nlines="158"/>
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	224 <expand macro="test_output_proteinorthograph" nlines="142"/>
1 26abc7846e6f "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5" iuc parents: 0 diff changeset	225 <assert_command>
26abc7846e6f "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5" iuc parents: 0 diff changeset	226 <has_text text="--p=blastp"/>
26abc7846e6f "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5" iuc parents: 0 diff changeset	227 </assert_command>
0 4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	228 </test>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	229 <test expect_num_outputs="3"> <!-- auto blast -->
5 5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	230 <param name="input_files" value="L.fasta,C.fasta,E.fasta,M.fasta"/>
1 26abc7846e6f "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5" iuc parents: 0 diff changeset	231 <param name="p" value="autoblast"/>
5 5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	232 <expand macro="test_output_proteinortho" nlines="32"/>
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	233 <expand macro="test_output_blastgraph" nlines="158"/>
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	234 <expand macro="test_output_proteinorthograph" nlines="142"/>
1 26abc7846e6f "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5" iuc parents: 0 diff changeset	235 <assert_command>
26abc7846e6f "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5" iuc parents: 0 diff changeset	236 <has_text text="--p=autoblast"/>
26abc7846e6f "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5" iuc parents: 0 diff changeset	237 </assert_command>
0 4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	238 </test>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	239 <test expect_num_outputs="3"> <!-- last -->
5 5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	240 <param name="input_files" value="L.fasta,C.fasta,E.fasta,M.fasta"/>
1 26abc7846e6f "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5" iuc parents: 0 diff changeset	241 <param name="p" value="lastp"/>
5 5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	242 <expand macro="test_output_proteinortho" nlines="34"/>
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	243 <expand macro="test_output_blastgraph" nlines="148"/>
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	244 <expand macro="test_output_proteinorthograph" nlines="133"/>
1 26abc7846e6f "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5" iuc parents: 0 diff changeset	245 <assert_command>
26abc7846e6f "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5" iuc parents: 0 diff changeset	246 <has_text text="--p=lastp"/>
26abc7846e6f "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5" iuc parents: 0 diff changeset	247 </assert_command>
0 4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	248 </test>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	249 <test expect_num_outputs="3"> <!-- blat -->
5 5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	250 <param name="input_files" value="L.fasta,C.fasta,E.fasta,M.fasta"/>
1 26abc7846e6f "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5" iuc parents: 0 diff changeset	251 <param name="p" value="blastp"/>
5 5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	252 <expand macro="test_output_proteinortho" nlines="32"/>
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	253 <expand macro="test_output_blastgraph" nlines="158"/>
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	254 <expand macro="test_output_proteinorthograph" nlines="142"/>
1 26abc7846e6f "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5" iuc parents: 0 diff changeset	255 <assert_command>
26abc7846e6f "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5" iuc parents: 0 diff changeset	256 <has_text text="--p=blastp"/>
26abc7846e6f "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5" iuc parents: 0 diff changeset	257 </assert_command>
0 4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	258 </test>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	259 </tests>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	260 <help><![CDATA[Proteinortho with POFF - An orthology detection tool
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	261
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	262 What it does
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	263
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	264 Proteinortho is a tool to detect orthologous proteins/genes within different species (at least 2).
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	265
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	266 \| It compares similarities of given gene/protein sequences and clusters them to find significant groups.
5 5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	267 \| The algorithm was designed to handle large-scale data and can be applied to hundreds of species at once.
0 4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	268 \| Details can be found in (doi:10.1186/1471-2105-12-124).
5 5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	269 \| To enhance the prediction accuracy, the relative order of genes (synteny) can be used as an additional feature for the discrimination of orthologs. The corresponding extension, namely PoFF (details see doi:10.1371/journal.pone.0105015), is already built in Proteinortho.
0 4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	270
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	271 ----
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	272
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	273 Proteinortho in a nutshell
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	274
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	275 ----
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	276
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	277 * (i) Build adaptive reciprocal best hit graph (RBH)
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	278
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	279 \| Using the blast algorithm (diamond,blast,blat,...) all input sequences are compared against each other.
5 5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	280 \| If two proteins find each other with respect to multiple criteria like minimal evalue, and similarity compared to the best hit, ... then an edge is drawn between the two proteins.
0 4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	281 \| The result of this step is outputted to RBH
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	282
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	283 * (ii) Cluster the RBH
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	284
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	285 \| Using two clustering algorithms, edges are removed that weakly connect two connected components to reduce false positive hits.
5 5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	286 \| The resulting connected components are outputted in orthology-groups / -pairs
0 4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	287
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	288 ----
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	289
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	290 Proteinortho output files
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	291
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	292 ----
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	293
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	294 * RBH
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	295
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	296 \| The result of the (i) step, the reciprocal best hit graph.
5 5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	297 \| First two comment line announces 2 species (# ecoli.faa human.faa) as well as the median values (evalue_ab,bitscore_ab,evalue_ba,bitscore_ba).
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	298 \| Following these header lines, each line corresponds to a reciprocal best hit of 2 proteins/genes (columns 1 and 2) of the announced species. The output format is shown below.
0 4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	299 \| seqidA,seqidB = the 2 ids/names of the proteins involved
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	300 \| evalue_ab = evalue with seqidA as query and seqidB as part of the database
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	301 \| bitscore_ab = bitscore with seqidA as query ...
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	302 \| evalue_ba = evalue with seqidB as query ...
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	303
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	304 .. csv-table::
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	305
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	306 seqidA,seqidB,evalue_ab,bitscore_ab,evalue_ba,bitscore_ba
5 5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	307 # ecoli.faa,human.faa
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	308 # 1.91e-112,357.5,1.825e-113,360
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	309 L_10,C_10;test,4.32e-151,447,4.30e-151,446
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	310 L_11,C_11,1.17e-68,209,3.00e-69,210
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	311 L_14,C_14,3.64e-139,422,1.19e-142,431
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	312 L_15,C_15,3.51e-100,303,2.12e-102,308
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	313 L_16,C_16,3.75e-49,157,7.06e-50,159
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	314 L_17,C_17,2.96e-195,578,5.50e-196,579
0 4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	315
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	316 ----
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	317
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	318 * orthology-groups
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	319
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	320 \| The result of the (ii) step, the clustered reciprocal best hit graph or the orthology groups.
5 5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	321 \| Every line corresponds to an orthology group.
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	322 \| The first 3 columns characterize the general properties of that group: number of proteins, species, and algebraic connectivity. The higher the algebraic connectivity the more edges are there and the better the group is connected to itself in general.
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	323 \| Then a column for each species follows containing the proteins of these species.
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	324 \| If a species contributes with more than one protein to a group of orthologs, then they are ordered by descending connectivity.
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	325 \| The '*' represents that this species does not contribute to the group.
0 4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	326
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	327 .. csv-table::
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	328
5 5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	329 Species,Genes,alg.-conn.,ecoli.faa,human.faa,snail.faa,wale.faa,ebola.faa
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	330 5,5,0.715,C_10,C_10;test,E_10,L_10,M_10
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	331 4,6,0.115,*,C_12,E_315,L_313,M_313
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	332 4,5,0.167,*,C_63,E_19,L_19,M_19
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	333 4,4,0.816,*,C_64,E_18,L_18,M_18
0 4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	334
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	335 ----
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	336
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	337 * orthology-pairs
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	338
5 5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	339 \| The same as orthology-groups but every edge is printed one-by-one instead of the whole group. The output is formatted the same as the RBH graph:
0 4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	340
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	341 .. csv-table::
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	342
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	343 seqidA,seqidB,evalue_ab,bitscore_ab,evalue_ba,bitscore_ba
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	344
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	345 ----
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	346
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	347 Proteinortho-Tools for downstream analysis
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	348
5 5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	349 * `proteinortho grab proteins` : find gene(s)/protein(s) in a given fasta file and retrieve their sequence(s). You can also use a orthology-groups file or a subset (e.g. filter by Species>10).
0 4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	350 * `proteinortho summary` : Summaries the orthology-pairs/RBH files to determine how the species are connected to each other.
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	351
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	352 More information can be found on github https://gitlab.com/paulklemm_PHD/proteinortho
5 5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	353
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	354 Citations:
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	355
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	356 - Lechner, Marcus, et al. "Proteinortho: detection of (co-) orthologs in large-scale analysis." BMC bioinformatics 12.1 (2011): 1-9. (10.1186/1471-2105-12-124)
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	357 - Lechner, Marcus, et al. "Orthology detection combining clustering and synteny for very large datasets." PLoS one 9.8 (2014): e105015. (10.1371/journal.pone.0105015)
5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	358
0 4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	359 ]]>
4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	360 </help>
5 5532c0e5d4a6 planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f iuc parents: 2 diff changeset	361 <expand macro="citations" /> <!--- TODO: citations are not working in usegalxy, therefore they are added manually at the above. -->
0 4850f0d15f01 "planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" iuc parents: diff changeset	362 </tool>

Mercurial > repos > iuc > proteinortho

annotate proteinortho.xml @ 6:10112d9127af draft