| Previous changeset 0:4850f0d15f01 (2020-02-18) Next changeset 2:a8addd4fb60a (2021-11-27) |
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Commit message:
"planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 95f1ae4ed1cdd56114df76d215f9e1ed549aa4c5" |
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modified:
proteinortho.xml proteinortho_macros.xml |
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| diff -r 4850f0d15f01 -r 26abc7846e6f proteinortho.xml --- a/proteinortho.xml Tue Feb 18 17:57:28 2020 -0500 +++ b/proteinortho.xml Tue Sep 14 11:39:10 2021 +0000 |
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| b'@@ -1,7 +1,32 @@\n-<tool id="proteinortho" name="Proteinortho" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@">\n+<tool id="proteinortho" name="Proteinortho" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@" profile="@PROFILE@">\n <description>detects orthologous proteins/genes within different species</description>\n <macros>\n <import>proteinortho_macros.xml</import>\n+ <xml name="test_outputs">\n+ <output name="proteinortho">\n+ <assert_contents>\n+ <has_line_matching expression="# Species\\tGenes\\tAlg\\.-Conn\\.\\t.*"/>\n+ <has_line_matching expression="[0-9]+\\t[0-9]+\\t.*"/>\n+ <has_line_matching expression=".*(C|C2|E|L|M)_[0-9]+.*"/>\n+ </assert_contents>\n+ </output>\n+ <output name="blastgraph">\n+ <assert_contents>\n+ <has_line_matching expression="# file_a\\tfile_b"/>\n+ <has_line_matching expression="# a\\tb\\tevalue_ab\\tbitscore_ab\\tevalue_ba\\tbitscore_ba"/>\n+ <has_line_matching expression="# (C|C2|E|L|M)\\.fasta\\t(C|C2|E|L|M)\\.fasta"/>\n+ <has_line_matching expression=".*(C|C2|E|L|M)_[0-9]+\\t(C|C2|E|L|M)_[0-9]+.*"/>\n+ </assert_contents>\n+ </output>\n+ <output name="proteinorthograph">\n+ <assert_contents>\n+ <has_line_matching expression="# file_a\\tfile_b"/>\n+ <has_line_matching expression="# a\\tb\\tevalue_ab\\tbitscore_ab\\tevalue_ba\\tbitscore_ba(\\tsame_strand\\tsimscore)?"/>\n+ <has_line_matching expression="# (C|C2|E|L|M)\\.fasta\\t(C|C2|E|L|M)\\.fasta"/>\n+ <has_line_matching expression=".*(C|C2|E|L|M)_[0-9]+\\t(C|C2|E|L|M)_[0-9]+.*"/>\n+ </assert_contents>\n+ </output>\n+ </xml>\n </macros>\n <expand macro="requirements"/>\n <expand macro="version_command"/>\n@@ -111,23 +136,10 @@\n <tests>\n <test expect_num_outputs="3"> <!-- test normal -->\n <param name="input_files" value="L.fasta,C.fasta,C2.fasta,E.fasta,M.fasta"/>\n- <output name="proteinortho">\n- <assert_contents>\n- <has_text text="# Species	Genes	Alg.-Conn."/>\n- <has_text text="2	5	0.16"/>\n- <has_text text="M_640,M_642,M_649"/>\n- </assert_contents>\n- </output>\n- <output name="blastgraph">\n- <assert_contents>\n- <has_text text="L_10	E_10	"/>\n- </assert_contents>\n- </output>\n- <output name="proteinorthograph">\n- <assert_contents>\n- <has_text text="L_11	E_11	"/>\n- </assert_contents>\n- </output>\n+ <expand macro="test_outputs"/>\n+ <assert_command>\n+ <has_text text="--p=diamond"/>\n+ </assert_command>\n </test>\n <test expect_num_outputs="3"> <!-- various parameter -->\n <param name="input_files" value="L.fasta,C.fasta,C2.fasta,E.fasta,M.fasta"/>\n@@ -138,124 +150,51 @@\n <param name="identity" value="42"/>\n <param name="selfblast" value="true"/>\n <param name="singles" value="true"/>\n- <output name="proteinortho">\n- <assert_contents>\n- <has_text text="# Species	Genes	Alg.-Conn."/>\n- <has_text text="1	1	0"/>\n- <has_text text="	C_177	"/>\n- </assert_contents>\n- </output>\n- <output name="blastgraph">\n- <assert_contents>\n- <has_text text="C_1	C_1	"/>\n- </assert_contents>\n- </output>\n- <output name="proteinorthograph">\n- <assert_contents>\n- '..b'_3	L_3	"/>\n- </assert_contents>\n- </output>\n- <output name="proteinorthograph">\n- <assert_contents>\n- <has_text text="M_317	L_317	"/>\n- </assert_contents>\n- </output>\n+ <param name="p" value="blastp"/>\n+ <expand macro="test_outputs"/>\n+ <assert_command>\n+ <has_text text="--p=blastp"/>\n+ </assert_command>\n </test>\n <test expect_num_outputs="3"> <!-- auto blast -->\n <param name="input_files" value="L.fasta,C.fasta,C2.fasta,E.fasta,M.fasta"/>\n- <param name="--p" value="autoblast"/>\n- <output name="proteinortho">\n- <assert_contents>\n- <has_text text="# Species	Genes	Alg.-Conn."/>\n- <has_text text="2	5	0.16"/>\n- <has_text text="M_640,M_642,M_649"/>\n- </assert_contents>\n- </output>\n- <output name="blastgraph">\n- <assert_contents>\n- <has_text text="M_3	L_3	"/>\n- </assert_contents>\n- </output>\n- <output name="proteinorthograph">\n- <assert_contents>\n- <has_text text="M_317	L_317	"/>\n- </assert_contents>\n- </output>\n+ <param name="p" value="autoblast"/>\n+ <expand macro="test_outputs"/>\n+ <assert_command>\n+ <has_text text="--p=autoblast"/>\n+ </assert_command>\n </test>\n <test expect_num_outputs="3"> <!-- last -->\n <param name="input_files" value="L.fasta,C.fasta,C2.fasta,E.fasta,M.fasta"/>\n- <param name="--p" value="lastp"/>\n- <output name="proteinortho">\n- <assert_contents>\n- <has_text text="# Species	Genes	Alg.-Conn."/>\n- <has_text text="2	5	0.16"/>\n- <has_text text="M_640,M_642,M_649"/>\n- </assert_contents>\n- </output>\n- <output name="blastgraph">\n- <assert_contents>\n- <has_text text="M_636	E_317	"/>\n- </assert_contents>\n- </output>\n- <output name="proteinorthograph">\n- <assert_contents>\n- <has_text text="E_11	C_11	"/>\n- </assert_contents>\n- </output>\n+ <param name="p" value="lastp"/>\n+ <expand macro="test_outputs"/>\n+ <assert_command>\n+ <has_text text="--p=lastp"/>\n+ </assert_command>\n </test>\n <test expect_num_outputs="3"> <!-- blat -->\n <param name="input_files" value="L.fasta,C.fasta,C2.fasta,E.fasta,M.fasta"/>\n- <param name="--p" value="blastp"/>\n- <output name="proteinortho">\n- <assert_contents>\n- <has_text text="# Species	Genes	Alg.-Conn."/>\n- <has_text text="2	5	0.16"/>\n- <has_text text="M_640,M_642,M_649"/>\n- </assert_contents>\n- </output>\n- <output name="blastgraph">\n- <assert_contents>\n- <has_text text="E_10	C_10	"/>\n- </assert_contents>\n- </output>\n- <output name="proteinorthograph">\n- <assert_contents>\n- <has_text text="E_10	C_10	"/>\n- </assert_contents>\n- </output>\n+ <param name="p" value="blastp"/>\n+ <expand macro="test_outputs"/>\n+ <assert_command>\n+ <has_text text="--p=blastp"/>\n+ </assert_command>\n </test>\n </tests>\n <help><![CDATA[Proteinortho with POFF - An orthology detection tool\n' |
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| diff -r 4850f0d15f01 -r 26abc7846e6f proteinortho_macros.xml --- a/proteinortho_macros.xml Tue Feb 18 17:57:28 2020 -0500 +++ b/proteinortho_macros.xml Tue Sep 14 11:39:10 2021 +0000 |
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| @@ -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"> |