Mercurial > repos > iuc > proteinortho
changeset 1:26abc7846e6f draft
"planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5"
author | iuc |
---|---|
date | Tue, 14 Sep 2021 11:39:10 +0000 (2021-09-14) |
parents | 4850f0d15f01 |
children | a8addd4fb60a |
files | proteinortho.xml proteinortho_macros.xml |
diffstat | 2 files changed, 67 insertions(+), 125 deletions(-) [+] |
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--- a/proteinortho.xml Tue Feb 18 17:57:28 2020 -0500 +++ b/proteinortho.xml Tue Sep 14 11:39:10 2021 +0000 @@ -1,7 +1,32 @@ -<tool id="proteinortho" name="Proteinortho" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@"> +<tool id="proteinortho" name="Proteinortho" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@" profile="@PROFILE@"> <description>detects orthologous proteins/genes within different species</description> <macros> <import>proteinortho_macros.xml</import> + <xml name="test_outputs"> + <output name="proteinortho"> + <assert_contents> + <has_line_matching expression="# Species\tGenes\tAlg\.-Conn\.\t.*"/> + <has_line_matching expression="[0-9]+\t[0-9]+\t.*"/> + <has_line_matching expression=".*(C|C2|E|L|M)_[0-9]+.*"/> + </assert_contents> + </output> + <output name="blastgraph"> + <assert_contents> + <has_line_matching expression="# file_a\tfile_b"/> + <has_line_matching expression="# a\tb\tevalue_ab\tbitscore_ab\tevalue_ba\tbitscore_ba"/> + <has_line_matching expression="# (C|C2|E|L|M)\.fasta\t(C|C2|E|L|M)\.fasta"/> + <has_line_matching expression=".*(C|C2|E|L|M)_[0-9]+\t(C|C2|E|L|M)_[0-9]+.*"/> + </assert_contents> + </output> + <output name="proteinorthograph"> + <assert_contents> + <has_line_matching expression="# file_a\tfile_b"/> + <has_line_matching expression="# a\tb\tevalue_ab\tbitscore_ab\tevalue_ba\tbitscore_ba(\tsame_strand\tsimscore)?"/> + <has_line_matching expression="# (C|C2|E|L|M)\.fasta\t(C|C2|E|L|M)\.fasta"/> + <has_line_matching expression=".*(C|C2|E|L|M)_[0-9]+\t(C|C2|E|L|M)_[0-9]+.*"/> + </assert_contents> + </output> + </xml> </macros> <expand macro="requirements"/> <expand macro="version_command"/> @@ -111,23 +136,10 @@ <tests> <test expect_num_outputs="3"> <!-- test normal --> <param name="input_files" value="L.fasta,C.fasta,C2.fasta,E.fasta,M.fasta"/> - <output name="proteinortho"> - <assert_contents> - <has_text text="# Species	Genes	Alg.-Conn."/> - <has_text text="2	5	0.16"/> - <has_text text="M_640,M_642,M_649"/> - </assert_contents> - </output> - <output name="blastgraph"> - <assert_contents> - <has_text text="L_10	E_10	"/> - </assert_contents> - </output> - <output name="proteinorthograph"> - <assert_contents> - <has_text text="L_11	E_11	"/> - </assert_contents> - </output> + <expand macro="test_outputs"/> + <assert_command> + <has_text text="--p=diamond"/> + </assert_command> </test> <test expect_num_outputs="3"> <!-- various parameter --> <param name="input_files" value="L.fasta,C.fasta,C2.fasta,E.fasta,M.fasta"/> @@ -138,124 +150,51 @@ <param name="identity" value="42"/> <param name="selfblast" value="true"/> <param name="singles" value="true"/> - <output name="proteinortho"> - <assert_contents> - <has_text text="# Species	Genes	Alg.-Conn."/> - <has_text text="1	1	0"/> - <has_text text="	C_177	"/> - </assert_contents> - </output> - <output name="blastgraph"> - <assert_contents> - <has_text text="C_1	C_1	"/> - </assert_contents> - </output> - <output name="proteinorthograph"> - <assert_contents> - <has_text text="C_12	C_21	"/> - </assert_contents> - </output> + <expand macro="test_outputs"/> + <assert_command> + <has_text text="--p=diamond"/> + </assert_command> </test> <test expect_num_outputs="3"> <!-- synteny --> <param name="input_files" value="L.fasta,C.fasta,C2.fasta,E.fasta,M.fasta"/> <param name="input_files_syn" value="L.gff,C.gff,C2.gff,E.gff,M.gff"/> <param name="synteny_options" value="specified"/> - <output name="proteinortho"> - <assert_contents> - <has_text text="# Species	Genes	Alg.-Conn."/> - <has_text text="4	5	0.144"/> - <has_text text="E_313,E_315"/> - </assert_contents> - </output> - <output name="proteinorthograph"> - <assert_contents> - <has_text text="M_313	L_313	"/> - </assert_contents> - </output> + <expand macro="test_outputs"/> + <assert_command> + <has_text text="--p=diamond"/> + </assert_command> </test> <test expect_num_outputs="3"> <!-- blast --> <param name="input_files" value="L.fasta,C.fasta,C2.fasta,E.fasta,M.fasta"/> - <param name="--p" value="blastp"/> - <output name="proteinortho"> - <assert_contents> - <has_text text="# Species	Genes	Alg.-Conn."/> - <has_text text="2	5	0.16"/> - <has_text text="M_640,M_642,M_649"/> - </assert_contents> - </output> - <output name="blastgraph"> - <assert_contents> - <has_text text="M_3	L_3	"/> - </assert_contents> - </output> - <output name="proteinorthograph"> - <assert_contents> - <has_text text="M_317	L_317	"/> - </assert_contents> - </output> + <param name="p" value="blastp"/> + <expand macro="test_outputs"/> + <assert_command> + <has_text text="--p=blastp"/> + </assert_command> </test> <test expect_num_outputs="3"> <!-- auto blast --> <param name="input_files" value="L.fasta,C.fasta,C2.fasta,E.fasta,M.fasta"/> - <param name="--p" value="autoblast"/> - <output name="proteinortho"> - <assert_contents> - <has_text text="# Species	Genes	Alg.-Conn."/> - <has_text text="2	5	0.16"/> - <has_text text="M_640,M_642,M_649"/> - </assert_contents> - </output> - <output name="blastgraph"> - <assert_contents> - <has_text text="M_3	L_3	"/> - </assert_contents> - </output> - <output name="proteinorthograph"> - <assert_contents> - <has_text text="M_317	L_317	"/> - </assert_contents> - </output> + <param name="p" value="autoblast"/> + <expand macro="test_outputs"/> + <assert_command> + <has_text text="--p=autoblast"/> + </assert_command> </test> <test expect_num_outputs="3"> <!-- last --> <param name="input_files" value="L.fasta,C.fasta,C2.fasta,E.fasta,M.fasta"/> - <param name="--p" value="lastp"/> - <output name="proteinortho"> - <assert_contents> - <has_text text="# Species	Genes	Alg.-Conn."/> - <has_text text="2	5	0.16"/> - <has_text text="M_640,M_642,M_649"/> - </assert_contents> - </output> - <output name="blastgraph"> - <assert_contents> - <has_text text="M_636	E_317	"/> - </assert_contents> - </output> - <output name="proteinorthograph"> - <assert_contents> - <has_text text="E_11	C_11	"/> - </assert_contents> - </output> + <param name="p" value="lastp"/> + <expand macro="test_outputs"/> + <assert_command> + <has_text text="--p=lastp"/> + </assert_command> </test> <test expect_num_outputs="3"> <!-- blat --> <param name="input_files" value="L.fasta,C.fasta,C2.fasta,E.fasta,M.fasta"/> - <param name="--p" value="blastp"/> - <output name="proteinortho"> - <assert_contents> - <has_text text="# Species	Genes	Alg.-Conn."/> - <has_text text="2	5	0.16"/> - <has_text text="M_640,M_642,M_649"/> - </assert_contents> - </output> - <output name="blastgraph"> - <assert_contents> - <has_text text="E_10	C_10	"/> - </assert_contents> - </output> - <output name="proteinorthograph"> - <assert_contents> - <has_text text="E_10	C_10	"/> - </assert_contents> - </output> + <param name="p" value="blastp"/> + <expand macro="test_outputs"/> + <assert_command> + <has_text text="--p=blastp"/> + </assert_command> </test> </tests> <help><![CDATA[Proteinortho with POFF - An orthology detection tool
--- a/proteinortho_macros.xml Tue Feb 18 17:57:28 2020 -0500 +++ b/proteinortho_macros.xml Tue Sep 14 11:39:10 2021 +0000 @@ -1,7 +1,8 @@ <?xml version="1.0"?> <macros> - <token name="@TOOL_VERSION@">6.0.14</token> - <token name="@WRAPPER_VERSION@">2.9.1</token> + <token name="@TOOL_VERSION@">6.0.31</token> + <token name="@WRAPPER_VERSION@">0</token> + <token name="@PROFILE@">20.09</token> <xml name="citations"> <citations> <citation type="doi">10.1186/1471-2105-12-124</citation> @@ -11,10 +12,12 @@ <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">proteinortho</requirement> - <requirement type="package">diamond</requirement> - <requirement type="package">blast</requirement> - <requirement type="package">blat</requirement> - <requirement type="package">last</requirement> + <!-- blast, blat, and last are not in the biopython requirements + diamond is, but latest version does not work: https://gitlab.com/paulklemm_PHD/proteinortho/-/issues/55 --> + <requirement type="package" version="2.0.9">diamond</requirement> + <requirement type="package" version="2.12.0">blast</requirement> + <requirement type="package" version="36">blat</requirement> + <requirement type="package" version="1256">last</requirement> </requirements> </xml> <xml name="version_command">