| Previous changeset 0:1b52f0c8ad7f (2021-01-03) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit 669dd4d406e86aee7d83e7420dced981c180d805 |
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modified:
macros.xml parseval.xml |
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| diff -r 1b52f0c8ad7f -r d6c074a93c51 macros.xml --- a/macros.xml Sun Jan 03 14:58:02 2021 +0000 +++ b/macros.xml Sun Feb 11 11:29:58 2024 +0000 |
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| @@ -9,12 +9,12 @@ </xml> <xml name="xrefs"> <xrefs> - <xref type='bio.tools'>gaeval</xref> + <xref type="bio.tools">gaeval</xref> </xrefs> </xml> <xml name="requirements"> <requirements> - <requirement type="package" version="0.16.0">aegean</requirement> + <requirement type="package" version="@TOOL_VERSION@">aegean</requirement> </requirements> </xml> <xml name="citations"> @@ -32,5 +32,5 @@ </citations> </xml> <token name="@TOOL_VERSION@">0.16.0</token> - + <token name="@VERSION_SUFFIX@">1</token> </macros> |
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| diff -r 1b52f0c8ad7f -r d6c074a93c51 parseval.xml --- a/parseval.xml Sun Jan 03 14:58:02 2021 +0000 +++ b/parseval.xml Sun Feb 11 11:29:58 2024 +0000 |
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| b'@@ -1,110 +1,110 @@\n-<tool id=\'aegean_parseval\' name=\'AEGeAn ParsEval\' version=\'@TOOL_VERSION@\' profile=\'20.01\'>\n+<tool id="aegean_parseval" name="AEGeAn ParsEval" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">\n <description> compare two sets of gene annotations for the same sequence.</description>\n <macros> \n <import>macros.xml</import>\n </macros> \n- <expand macro=\'xrefs\'/>\n- <expand macro=\'edam_ontology\'/>\n- <expand macro=\'requirements\'/>\n+ <expand macro="edam_ontology"/>\n+ <expand macro="xrefs"/>\n+ <expand macro="requirements"/>\n <version_command>parseval --version</version_command>\n- <command detect_errors=\'exit_code\'>\n+ <command detect_errors="exit_code">\n <![CDATA[\n- #if $output_type == \'html\'\n- mkdir -p \'${output_html.extra_files_path}\' &&\n+ #if $output_type == "html"\n+ mkdir -p "${output_html.extra_files_path}" &&\n #end if\n- parseval \'$referencegff3\' \'$predictiongff3\' \n+ parseval "$referencegff3" "$predictiongff3" \n --delta $delta\n --maxtrans $maxtrans\n -w\n #if $refrlabel\n- --refrlabel \'$refrlabel\'\n+ --refrlabel "$refrlabel"\n #end if\n #if $predlabel\n- --predlabel \'$predlabel\'\n+ --predlabel "$predlabel"\n #end if\n- #if $output_type ==\'text\'\n- -f \'text\'\n- -o \'$output_txt\'\n- #else if $output_type == \'html\'\n- -f \'html\' \n- -o \'${output_html.files_path}\' &&\n- echo "</div> </body> </html>" >> \'${output_html.files_path}\'/index.html &&\n- cp \'${output_html.files_path}\'/index.html \'$output_html\'\n+ #if $output_type =="text"\n+ -f "text"\n+ -o "$output_txt"\n+ #else if $output_type == "html"\n+ -f "html" \n+ -o "${output_html.files_path}" &&\n+ echo "</div> </body> </html>" >> "${output_html.files_path}"/index.html &&\n+ cp "${output_html.files_path}"/index.html "$output_html"\n #end if\n ]]>\n </command>\n <inputs>\n- <param name=\'referencegff3\' type=\'data\' format=\'gff3\' label="Reference GFF3 file"/>\n- <param name=\'predictiongff3\' type=\'data\' format=\'gff3\' label="Prediction GFF3 file"/>\n- <param argument=\'--delta\' type=\'integer\'\n- min=\'0\' max=\'20\' value=\'0\' \n- label=\'Number of nucleotides to extend gene loci\'/>\n- <param argument=\'--maxtrans\' type=\'integer\' \n- min=\'1\' max=\'50\' value=\'32\'\n- label=\'Maximum transcript allowed per locus\' />\n- <param name=\'output_type\' type=\'select\'\n- label=\'Select the output type\'>\n- <option value=\'text\'>Text</option>\n- <option value=\'html\'>HTML</option>\n+ <param name="referencegff3" type="data" format="gff3" label="Reference GFF3 file"/>\n+ <param name="predictiongff3" type="data" format="gff3" label="Prediction GFF3 file"/>\n+ <param argument="--delta" type="integer"\n+ min="0" max="20" value="0" \n+ label="Number of nucleotides to extend gene loci"/>\n+ <param argument="--maxtrans" type="integer" \n+ min="1" max="50" value="32"\n+ label="Maximum transcript allowed per locus" />\n+ <param name="output_type" type="select"\n+ label="Select the output type">\n+ <option value="text">Text</option>\n+ <option value="html">HTML</option>\n </param>\n- <param argument=\'--refrlabel\' type=\'text\'\n- value=\'\' optional=\'true\'\n- label=\'Reference annotati'..b'20"/>\n+ <output name="output_txt" file="parseval_output_test1.txt" lines_diff="8"/>\n </test>\n <test expect_num_outputs="1">\n- <param name=\'referencegff3\' value=\'TAIR9_GFF3_genes.gff\'/>\n- <param name=\'predictiongff3\' value=\'TAIR10_GFF3_genes.gff\'/>\n- <output name=\'output_txt\' file=\'parseval_output_test2.txt\' lines_diff=\'8\'/>\n+ <param name="referencegff3" value="TAIR9_GFF3_genes.gff" ftype="gff3"/>\n+ <param name="predictiongff3" value="TAIR10_GFF3_genes.gff" ftype="gff3"/>\n+ <output name="output_txt" file="parseval_output_test2.txt" lines_diff="8"/>\n </test>\n <test expect_num_outputs="1">\n- <param name=\'referencegff3\' value=\'TAIR9_GFF3_genes.gff\'/>\n- <param name=\'predictiongff3\' value=\'TAIR10_GFF3_genes.gff\'/>\n- <param name=\'delta\' value=\'10\'/>\n- <param name=\'maxtrans\' value=\'10\'/>\n- <output name=\'output_txt\' file=\'parseval_output_test3.txt\' lines_diff=\'8\'/>\n+ <param name="referencegff3" value="TAIR9_GFF3_genes.gff" ftype="gff3"/>\n+ <param name="predictiongff3" value="TAIR10_GFF3_genes.gff" ftype="gff3"/>\n+ <param name="delta" value="10"/>\n+ <param name="maxtrans" value="10"/>\n+ <output name="output_txt" file="parseval_output_test3.txt" lines_diff="8"/>\n </test>\n <test expect_num_outputs="1">\n- <param name=\'referencegff3\' value=\'TAIR9_GFF3_genes.gff\'/>\n- <param name=\'predictiongff3\' value=\'TAIR10_GFF3_genes.gff\'/>\n- <param name=\'output_type\' value=\'html\'/>\n- <output name=\'output_html\' file=\'parseval_output_test4.html\' lines_diff=\'8\'/>\n+ <param name="referencegff3" value="TAIR9_GFF3_genes.gff" ftype="gff3"/>\n+ <param name="predictiongff3" value="TAIR10_GFF3_genes.gff" ftype="gff3"/>\n+ <param name="output_type" value="html"/>\n+ <output name="output_html" file="parseval_output_test4.html" lines_diff="8"/>\n </test>\n <test expect_num_outputs="1">\n- <param name=\'referencegff3\' value=\'TAIR9_GFF3_genes.gff\'/>\n- <param name=\'predictiongff3\' value=\'TAIR10_GFF3_genes.gff\'/>\n- <param name=\'output_type\' value=\'html\'/>\n- <param name=\'delta\' value=\'10\'/>\n- <param name=\'maxtrans\' value=\'10\'/>\n- <output name=\'output_html\' file=\'parseval_output_test5.html\' lines_diff=\'8\'/>\n+ <param name="referencegff3" value="TAIR9_GFF3_genes.gff" ftype="gff3"/>\n+ <param name="predictiongff3" value="TAIR10_GFF3_genes.gff" ftype="gff3"/>\n+ <param name="output_type" value="html"/>\n+ <param name="delta" value="10"/>\n+ <param name="maxtrans" value="10"/>\n+ <output name="output_html" file="parseval_output_test5.html" lines_diff="8"/>\n </test>\n <test expect_num_outputs="1">\n- <param name=\'referencegff3\' value=\'TAIR9_GFF3_genes.gff\'/>\n- <param name=\'predictiongff3\' value=\'TAIR10_GFF3_genes.gff\'/>\n- <param name=\'output_type\' value=\'text\'/>\n- <param name=\'refrlabel\' value=\'example_ref_label\'/>\n- <param name=\'predlabel\' value=\'example_pred_label\'/>\n- <output name=\'output_txt\' file=\'parseval_output_test6.txt\' lines_diff=\'8\'/>\n+ <param name="referencegff3" value="TAIR9_GFF3_genes.gff" ftype="gff3"/>\n+ <param name="predictiongff3" value="TAIR10_GFF3_genes.gff" ftype="gff3"/>\n+ <param name="output_type" value="text"/>\n+ <param name="refrlabel" value="example_ref_label"/>\n+ <param name="predlabel" value="example_pred_label"/>\n+ <output name="output_txt" file="parseval_output_test6.txt" lines_diff="8"/>\n </test>\n </tests>\n <help>\n@@ -144,5 +144,5 @@\n \n ]]>\n </help>\n- <expand macro=\'citations\'/>\n+ <expand macro="citations"/>\n </tool>\n' |