| Previous changeset 6:10112d9127af (2023-10-31) Next changeset 8:54fb02338510 (2024-03-06) |
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Commit message:
planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 5eba1fb52a5ec1e63ca126be42062323e1a76687 |
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modified:
proteinortho.xml proteinortho_macros.xml |
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| diff -r 10112d9127af -r c5dd4f86d981 proteinortho.xml --- a/proteinortho.xml Tue Oct 31 16:32:03 2023 +0000 +++ b/proteinortho.xml Tue Jan 23 12:21:52 2024 +0000 |
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| b'@@ -2,24 +2,24 @@\n <description>detects orthologous proteins/genes within different species</description>\n <macros>\n <import>proteinortho_macros.xml</import>\n- <xml name="test_output_proteinortho" tokens="nlines">\n+ <xml name="test_output_proteinortho" tokens="nlines" token_nlines_delta="0">\n <output name="proteinortho">\n <metadata name="column_names" value="species,genes,alg.-conn.,L.fasta,C.fasta,E.fasta,M.fasta"/>\n <assert_contents>\n <has_n_columns n="7"/>\n- <has_n_lines n="@NLINES@"/>\n+ <has_n_lines n="@NLINES@" delta="@NLINES_DELTA@"/>\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 </xml>\n- <xml name="test_output_blastgraph" tokens="nlines">\n+ <xml name="test_output_blastgraph" tokens="nlines" token_nlines_delta="0">\n <output name="blastgraph">\n <metadata name="column_names" value="seqidA,seqidB,evalue_ab,bitscore_ab,evalue_ba,bitscore_ba"/>\n <assert_contents>\n <has_n_columns n="6" comment="#"/>\n- <has_n_lines n="@NLINES@"/>\n+ <has_n_lines n="@NLINES@" delta="@NLINES_DELTA@"/>\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@@ -97,6 +97,10 @@\n #end for#\n #end if\n 2> >(sed -E "s/.\\[([0-9]{1,2}(;[0-9]{1,2})?)?[mGK]//g" 1>&2)\n+ #if $more_options.selfblast:\n+ &&\n+ mv result.blast-graph_clean result.blast-graph;\n+ #end if\n #if $synteny.synteny_options == "specified":\n &&\n mv result.poff-graph result.proteinortho-graph &&\n@@ -176,9 +180,9 @@\n <test expect_num_outputs="3"> <!-- test normal -->\n <param name="input_files" value="L.fasta,C.fasta,E.fasta,M.fasta"/>\n <param name="p" value="diamond"/>\n- <expand macro="test_output_proteinortho" nlines="34"/>\n- <expand macro="test_output_blastgraph" nlines="157"/>\n- <expand macro="test_output_proteinorthograph" nlines="134"/>\n+ <expand macro="test_output_proteinortho" nlines="33" nlines_delta="5"/>\n+ <expand macro="test_output_blastgraph" nlines="156" nlines_delta="20"/>\n+ <expand macro="test_output_proteinorthograph" nlines="139" nlines_delta="20"/>\n <assert_command>\n <has_text text="--p=diamond"/>\n </assert_command>\n@@ -191,13 +195,12 @@\n <section name="more_options">\n <param name="cov" value="42"/>\n <param name="identity" value="42"/>\n- <param name="selfblast" value="true"/>\n <param name="singles" value="true"/>\n <param name="core" value="true"/>\n </section>\n- <expand macro="test_output_proteinortho" nlines="177"/>\n- <expand macro="test_output_blastgraph" nlines="2720"/>\n- <expand macro="test_output_proteinorthograph" nlines="384"/>\n+ <expand macro="test_output_proteinortho" nlines="151" nlines_delta="50"/>\n+ <expand macro="test_output_blastgraph" nlines="1403" nlines_delta="300"/>\n+ <expand macro="test_output_proteinorthograph" nlines="239" nlines_delta="150"/>\n <assert_command>\n <has_text text="--p=diamond"/>\n </assert_command>\n@@ -209,8 +212,8 @@\n <conditional name="synteny">\n '..b' <expand macro="test_output_proteinorthograph" nlines="142"/>\n+ <expand macro="test_output_proteinortho" nlines="33" nlines_delta="20"/>\n+ <expand macro="test_output_blastgraph" nlines="155" nlines_delta="50"/>\n+ <expand macro="test_output_proteinorthograph" nlines="139" nlines_delta="50"/>\n <assert_command>\n <has_text text="--p=blastp"/>\n </assert_command>\n@@ -229,9 +232,9 @@\n <test expect_num_outputs="3"> <!-- auto blast -->\n <param name="input_files" value="L.fasta,C.fasta,E.fasta,M.fasta"/>\n <param name="p" value="autoblast"/>\n- <expand macro="test_output_proteinortho" nlines="32"/>\n- <expand macro="test_output_blastgraph" nlines="158"/>\n- <expand macro="test_output_proteinorthograph" nlines="142"/>\n+ <expand macro="test_output_proteinortho" nlines="33" nlines_delta="20"/>\n+ <expand macro="test_output_blastgraph" nlines="157" nlines_delta="50"/>\n+ <expand macro="test_output_proteinorthograph" nlines="136" nlines_delta="50"/>\n <assert_command>\n <has_text text="--p=autoblast"/>\n </assert_command>\n@@ -239,9 +242,9 @@\n <test expect_num_outputs="3"> <!-- last -->\n <param name="input_files" value="L.fasta,C.fasta,E.fasta,M.fasta"/>\n <param name="p" value="lastp"/>\n- <expand macro="test_output_proteinortho" nlines="34"/>\n- <expand macro="test_output_blastgraph" nlines="148"/>\n- <expand macro="test_output_proteinorthograph" nlines="133"/>\n+ <expand macro="test_output_proteinortho" nlines="34" nlines_delta="20"/>\n+ <expand macro="test_output_blastgraph" nlines="148" nlines_delta="50"/>\n+ <expand macro="test_output_proteinorthograph" nlines="134" nlines_delta="50"/>\n <assert_command>\n <has_text text="--p=lastp"/>\n </assert_command>\n@@ -249,9 +252,9 @@\n <test expect_num_outputs="3"> <!-- blat -->\n <param name="input_files" value="L.fasta,C.fasta,E.fasta,M.fasta"/>\n <param name="p" value="blastp"/>\n- <expand macro="test_output_proteinortho" nlines="32"/>\n- <expand macro="test_output_blastgraph" nlines="158"/>\n- <expand macro="test_output_proteinorthograph" nlines="142"/>\n+ <expand macro="test_output_proteinortho" nlines="33" nlines_delta="20"/>\n+ <expand macro="test_output_blastgraph" nlines="156" nlines_delta="50"/>\n+ <expand macro="test_output_proteinorthograph" nlines="136" nlines_delta="50"/>\n <assert_command>\n <has_text text="--p=blastp"/>\n </assert_command>\n@@ -265,7 +268,7 @@\n \n | It compares similarities of given gene/protein sequences and clusters them to find significant groups.\n | The algorithm was designed to handle large-scale data and can be applied to hundreds of species at once.\n- | Details can be found in (doi:10.1186/1471-2105-12-124).\n+ | Details can be found in (doi:10.1186/1471-2105-12-124 and doi:10.3389/fbinf.2023.1322477).\n | 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. \n \n ----\n@@ -353,9 +356,6 @@\n \n **Citations:**\n \n-- 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) \n-- 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)\n-\n ]]>\n </help>\n <expand macro="citations" /> <!--- TODO: citations are not working in usegalxy, therefore they are added manually at the above. -->\n' |
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| diff -r 10112d9127af -r c5dd4f86d981 proteinortho_macros.xml --- a/proteinortho_macros.xml Tue Oct 31 16:32:03 2023 +0000 +++ b/proteinortho_macros.xml Tue Jan 23 12:21:52 2024 +0000 |
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| @@ -1,12 +1,13 @@ <?xml version="1.0"?> <macros> - <token name="@TOOL_VERSION@">6.2.3</token> + <token name="@TOOL_VERSION@">6.3.1</token> <token name="@WRAPPER_VERSION@">2</token> <token name="@PROFILE@">20.09</token> <xml name="citations"> <citations> <citation type="doi">10.1186/1471-2105-12-124</citation> <citation type="doi">10.1371/journal.pone.0105015</citation> + <citation type="doi">10.3389/fbinf.2023.1322477</citation> </citations> </xml> <xml name="biotools"> |