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(-) [+]
line wrap: on
line diff
--- 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>