Mercurial > repos > greg > vsnp_get_snps
changeset 14:44b84d32883c draft default tip
"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
| author | greg |
|---|---|
| date | Mon, 15 Nov 2021 23:14:34 +0000 |
| parents | cd636b0e4f95 |
| children | |
| files | macros.xml test-data/Mbovis-17_avg_mq_json.json test-data/Mbovis-17_snps.fasta test-data/Mbovis-17_snps_json.json test-data/all_vcf.fasta test-data/all_vcf2.fasta test-data/json_all_vcf.json test-data/json_avg_mq_all_vcf.json test-data/output_summary.html test-data/output_summary2.html test-data/output_summary3.html test-data/output_summary4.html vsnp_get_snps.xml |
| diffstat | 13 files changed, 97 insertions(+), 87 deletions(-) [+] |
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--- a/macros.xml Tue Sep 21 00:21:36 2021 +0000 +++ b/macros.xml Mon Nov 15 23:14:34 2021 +0000 @@ -9,7 +9,7 @@ <requirement type="package" version="1.21.1">numpy</requirement> </xml> <xml name="openpyxl_requirement"> - <requirement type="package" version="3.0.7">openpyxl</requirement> + <requirement type="package" version="3.0.9">openpyxl</requirement> </xml> <xml name="pandas_requirement"> <requirement type="package" version="1.3.0">pandas</requirement>
--- a/test-data/Mbovis-17_avg_mq_json.json Tue Sep 21 00:21:36 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -{"name"
--- a/test-data/Mbovis-17_snps.fasta Tue Sep 21 00:21:36 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ ->01_1787_FL_Zoo_Jaguar_vcf ->02_0585_COA_TX_Fed_vcf ->02_5877_MEX_TX_Fed_vcf ->root
--- a/test-data/Mbovis-17_snps_json.json Tue Sep 21 00:21:36 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -{"columns":
--- a/test-data/all_vcf.fasta Tue Sep 21 00:21:36 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ ->SRR1792272_zc ->input_zc ->SRR8073662_zc ->root
--- a/test-data/all_vcf2.fasta Tue Sep 21 00:21:36 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ ->01_1787_FL_Zoo_Jaguar_vcf ->BCG_Pasteur_Unknown_FR_SRR8886989_vcf ->02_0585_COA_TX_Fed_vcf ->BCG_Tokyo_Unknown_JP_DRR029468_vcf ->02_5877_MEX_TX_Fed_vcf ->root
--- a/test-data/json_all_vcf.json Tue Sep 21 00:21:36 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -{"columns":[
--- a/test-data/json_avg_mq_all_vcf.json Tue Sep 21 00:21:36 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -{"name":null,"index":[
--- a/test-data/output_summary.html Tue Sep 21 00:21:36 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -<html> -<head></head> -<br/><b>Number of VCF inputs:</b> 3<br/><b>Reference:</b> -<br/><b>Total run time:</b> -</body> -</html>
--- a/test-data/output_summary2.html Tue Sep 21 00:21:36 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5 +0,0 @@ -<html> -<head></head> -Number of VCF inputs:</b> 5<br/><b>Reference:</b> 89<br/><b>All isolates:</b> False<br/><br/><b> -</body> -</html>
--- a/test-data/output_summary3.html Tue Sep 21 00:21:36 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,18 +0,0 @@ -<html> -<head></head> -<b>Number of VCF inputs:</b> 5<br/><b>Reference:</b> 89<br/><b>All isolates:</b> False<br/><br/><b>Groupings with 5 listed:</b><br/> -<td>01_1787_FL_Zoo_Jaguar_vcf</td><td>Mbovis-17</td> -<td>Mbovis-17G</td> -<td>BCG_Pasteur_Unknown_FR_SRR8886989_vcf</td><td>Mbovis-21</td> -<td>Mbovis-21A</td> -<td>Mbovis-21ABCG</td> -<td>02_0585_COA_TX_Fed_vcf</td><td>Mbovis-17</td> -<td>Mbovis-17A</td> -<td>BCG_Tokyo_Unknown_JP_DRR029468_vcf</td><td>Mbovis-21</td> -<td>Mbovis-21A</td> -<td>Mbovis-21ABCG</td> -<td>02_5877_MEX_TX_Fed_vcf</td><td>Mbovis-17</td> -<td>Mbovis-17A</td> -</table><br/> -</body> -</html>
--- a/test-data/output_summary4.html Tue Sep 21 00:21:36 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,19 +0,0 @@ -<html> -<head></head> -Number of VCF inputs:</b> 5<br/><b>Reference:</b> 89<br/><b>All isolates:</b> True<br/><br/><b>Groupings with 5 listed:</b><br/> -<table cellpadding="5" cellspaging="5" border="1"> -<td>01_1787_FL_Zoo_Jaguar_vcf</td><td>Mbovis-17</td> -<td>Mbovis-17G</td> -<td>BCG_Pasteur_Unknown_FR_SRR8886989_vcf</td><td>Mbovis-21</td> -<td>Mbovis-21A</td> -<td>Mbovis-21ABCG</td> -<td>02_0585_COA_TX_Fed_vcf</td><td>Mbovis-17</td> -<td>Mbovis-17A</td> -<td>BCG_Tokyo_Unknown_JP_DRR029468_vcf</td><td>Mbovis-21</td> -<td>Mbovis-21A</td> -<td>Mbovis-21ABCG</td> -<td>02_5877_MEX_TX_Fed_vcf</td><td>Mbovis-17</td> -<td>Mbovis-17A</td> -</table><br/> -</body> -</html>
--- a/vsnp_get_snps.xml Tue Sep 21 00:21:36 2021 +0000 +++ b/vsnp_get_snps.xml Mon Nov 15 23:14:34 2021 +0000 @@ -131,7 +131,7 @@ </when> <when value="no"/> </conditional> - <param argument="all_isolates" type="boolean" truevalue="--all_isolates" falsevalue="" checked="true" label="Create a group containing all isolates?"/> + <param name="all_isolates" type="boolean" truevalue="--all_isolates" falsevalue="" checked="true" label="Create a group containing all isolates?"/> </inputs> <outputs> <collection name="snps" type="list" label="${tool.name} on ${on_string} (SNPs)"> @@ -166,15 +166,31 @@ <param name="input_excel_param" value="no"/> <param name="all_isolates" value=""/> <output_collection name="snps" type="list" count="1"> - <element name="all_vcf" file="all_vcf.fasta" ftype="fasta" compare="contains"/> + <element name="all_vcf" ftype="fasta"> + <assert_contents> + <has_size value="150"/> + </assert_contents> + </element> </output_collection> <output_collection name="json_avg_mq" type="list" count="1"> - <element name="all_vcf" file="json_avg_mq_all_vcf.json" ftype="json" compare="contains"/> + <element name="all_vcf" ftype="json"> + <assert_contents> + <has_size value="551"/> + </assert_contents> + </element> </output_collection> <output_collection name="json_snps" type="list" count="1"> - <element name="all_vcf" file="json_all_vcf.json" ftype="json" compare="contains"/> + <element name="all_vcf" ftype="json"> + <assert_contents> + <has_size value="876"/> + </assert_contents> + </element> </output_collection> - <output name="output_summary" file="output_summary.html" ftype="html" compare="contains"/> + <output name="output_summary" ftype="html"> + <assert_contents> + <has_size value="303"/> + </assert_contents> + </output> </test> <!-- An input collection, no excel file, all_isolates is False --> <test expect_num_outputs="4"> @@ -196,15 +212,31 @@ <param name="input_excel_param" value="no"/> <param name="all_isolates" value=""/> <output_collection name="snps" type="list" count="1"> - <element name="all_vcf" file="all_vcf2.fasta" ftype="fasta" compare="contains"/> + <element name="all_vcf" ftype="fasta"> + <assert_contents> + <has_size value="5226"/> + </assert_contents> + </element> </output_collection> <output_collection name="json_avg_mq" type="list" count="1"> - <element name="all_vcf" file="json_avg_mq_all_vcf.json" ftype="json" compare="contains"/> + <element name="all_vcf" ftype="json"> + <assert_contents> + <has_size value="24332"/> + </assert_contents> + </element> </output_collection> <output_collection name="json_snps" type="list" count="1"> - <element name="all_vcf" file="json_all_vcf.json" ftype="json" compare="contains"/> + <element name="all_vcf" ftype="json"> + <assert_contents> + <has_size value="38798"/> + </assert_contents> + </element> </output_collection> - <output name="output_summary" file="output_summary2.html" ftype="html" compare="contains"/> + <output name="output_summary" ftype="html"> + <assert_contents> + <has_size value="303"/> + </assert_contents> + </output> </test> <!-- An input collection, an excel file, all_isolates is False --> <test expect_num_outputs="4"> @@ -227,15 +259,31 @@ <param name="input_excel" value="89"/> <param name="all_isolates" value=""/> <output_collection name="snps" type="list" count="1"> - <element name="Mbovis-17" file="Mbovis-17_snps.fasta" ftype="fasta" compare="contains"/> + <element name="Mbovis-17" ftype="fasta"> + <assert_contents> + <has_size value="749"/> + </assert_contents> + </element> </output_collection> <output_collection name="json_avg_mq" type="list" count="1"> - <element name="Mbovis-17" file="Mbovis-17_avg_mq_json.json" ftype="json" compare="contains"/> + <element name="Mbovis-17" ftype="json"> + <assert_contents> + <has_size value="10884"/> + </assert_contents> + </element> </output_collection> <output_collection name="json_snps" type="list" count="1"> - <element name="Mbovis-17" file="Mbovis-17_snps_json.json" ftype="json" compare="contains"/> + <element name="Mbovis-17" ftype="json"> + <assert_contents> + <has_size value="6396"/> + </assert_contents> + </element> </output_collection> - <output name="output_summary" file="output_summary3.html" ftype="html" compare="contains"/> + <output name="output_summary" ftype="html"> + <assert_contents> + <has_size value="1057"/> + </assert_contents> + </output> </test> <!-- An input collection, an excel file, all_isolates is True --> <test expect_num_outputs="4"> @@ -258,18 +306,46 @@ <param name="input_excel" value="89"/> <param name="all_isolates" value="--all_isolates"/> <output_collection name="snps" type="list" count="2"> - <element name="Mbovis-17" file="Mbovis-17_snps.fasta" ftype="fasta" compare="contains"/> - <element name="all_vcf" file="all_vcf2.fasta" ftype="fasta" compare="contains"/> + <element name="Mbovis-17" ftype="fasta"> + <assert_contents> + <has_size value="749"/> + </assert_contents> + </element> + <element name="all_vcf" ftype="fasta"> + <assert_contents> + <has_size value="4920"/> + </assert_contents> + </element> </output_collection> <output_collection name="json_avg_mq" type="list" count="2"> - <element name="Mbovis-17" file="Mbovis-17_avg_mq_json.json" ftype="json" compare="contains"/> - <element name="all_vcf" file="Mbovis-17_avg_mq_json.json" ftype="json" compare="contains"/> + <element name="Mbovis-17" ftype="json"> + <assert_contents> + <has_size value="10884"/> + </assert_contents> + </element> + <element name="all_vcf" ftype="json"> + <assert_contents> + <has_size value="24332"/> + </assert_contents> + </element> </output_collection> <output_collection name="json_snps" type="list" count="2"> - <element name="Mbovis-17" file="Mbovis-17_snps_json.json" ftype="json" compare="contains"/> - <element name="all_vcf" file="Mbovis-17_snps_json.json" ftype="json" compare="contains"/> + <element name="Mbovis-17" ftype="json"> + <assert_contents> + <has_size value="6396"/> + </assert_contents> + </element> + <element name="all_vcf" ftype="json"> + <assert_contents> + <has_size value="36466"/> + </assert_contents> + </element> </output_collection> - <output name="output_summary" file="output_summary4.html" ftype="html" compare="contains"/> + <output name="output_summary" ftype="html"> + <assert_contents> + <has_size value="1056"/> + </assert_contents> + </output> </test> </tests> <help>