Mercurial > repos > greg > vsnp_get_snps

diff vsnp_get_snps.xml @ 14:44b84d32883c draft default tip

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"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
line wrap: on
line diff
--- 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>