Mercurial > repos > dfornika > tetyper

changeset 24:ea14ef930fc5 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 3803eff127b827b669627f7a529e84142812fc56-dirty"
author dfornika
date Fri, 10 Jan 2020 18:52:22 +0000
parents 7158a1df3841
children 98d8bd5e9058
files test-data/tetyper_snp_profiles.loc test-data/tetyper_struct_profiles.loc tetyper.xml tool_data_table_conf.xml.test
diffstat 4 files changed, 58 insertions(+), 14 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tetyper_snp_profiles.loc	Fri Jan 10 18:52:22 2020 +0000
@@ -0,0 +1,6 @@
+# Tab separated with three columns:
+# - value (Galaxy records this in the Galaxy DB)
+# - name (Galaxy shows this in the UI)
+# - path (path to the snp_profiles.txt file)
+#
+Tn4401b_snp_profiles	"Tn4401b SNP Profiles"	${__HERE__}/Tn4401b_snp_profiles.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tetyper_struct_profiles.loc	Fri Jan 10 18:52:22 2020 +0000
@@ -0,0 +1,6 @@
+# Tab separated with three columns:
+# - value (Galaxy records this in the Galaxy DB)
+# - name (Galaxy shows this in the UI)
+# - path (path to the struct_profiles.txt file)
+#
+Tn4401b_struct_profiles	"Tn4401b Structural Variant Profiles"	${__HERE__}/Tn4401b_struct_profiles.txt
--- a/tetyper.xml	Sat Jan 04 00:48:57 2020 +0000
+++ b/tetyper.xml	Fri Jan 10 18:52:22 2020 +0000
@@ -55,34 +55,32 @@
             </when>
         </conditional>
         <conditional name="snp_profiles_source">
-            <param name="snp_profiles_source_selector" type="select" label="Select a SNP profile from your history or use one from a tool data table?"
-                   help="Screening files must be stored in the 'tetyper_snp_profiles' tool data table">
+            <param name="snp_profiles_source_selector" type="select" label="Select a SNP profile from your history or use one from a tool data table?">
                 <option value="tool_data_table">From tool data table</option>
                 <option value="history" selected="true">From history</option>
             </param>
             <when value="tool_data_table">
-                <param name="snp_profiles" type="select" format="tabular">
-	            <options from_data_table="tetyper_snp_profiles">
-	                <validator type="no_options" message="No TETyper SNP profiles are available" />
+                <param name="snp_profiles" type="select" format="tabular" optional="true">
+                    <options from_data_table="tetyper_snp_profiles">
+                        <validator type="no_options" message="No TETyper SNP profiles are available" />
                     </options>
-	        </param>
+                </param>
             </when>
             <when value="history">
                 <param name="snp_profiles" type="data" format="tabular" label="SNP Profile" help="A three-column tabular file with SNP profile definitions" optional="true"/>
             </when>
         </conditional>
         <conditional name="struct_profiles_source">
-            <param name="struct_profiles_source_selector" type="select" label="Select a structural variant profile from your history or use one from a tool data table?"
-                   help="Files must be stored in the 'tetyper_struct_profiles' tool data table">
+            <param name="struct_profiles_source_selector" type="select" label="Select a structural variant profile from your history or use one from a tool data table?">
                 <option value="tool_data_table">From tool data table</option>
                 <option value="history" selected="true">From history</option>
             </param>
             <when value="tool_data_table">
-                <param name="struct_profiles" type="select" format="tabular">
-	            <options from_data_table="tetyper_struct_profiles">
-	                <validator type="no_options" message="No TETyper structural variant profiles are available" />
+                <param name="struct_profiles" type="select" format="tabular" optional="true">
+                    <options from_data_table="tetyper_struct_profiles">
+                        <validator type="no_options" message="No TETyper structural variant profiles are available" />
                     </options>
-	        </param>
+                </param>
             </when>
             <when value="history">
                 <param name="struct_profiles" type="data" format="tabular" label="Structural Variant Profile" help="A two-column tabular file with structural variant profile definitions" optional="true"/>
@@ -122,8 +120,31 @@
                 <param name="forward_input" value="ERR1911133_Tn4401b-1_mapped_subsampled_1.fastq" />
                 <param name="reverse_input" value="ERR1911133_Tn4401b-1_mapped_subsampled_2.fastq" />
             </conditional>
-            <param name="snp_profiles" value="Tn4401b_snp_profiles.txt" />
-            <param name="struct_profiles" value="Tn4401b_struct_profiles.txt" />
+            <conditional name="snp_profiles_source">
+                <param name="snp_profiles_source_selector" value="history" />
+                <param name="snp_profiles" value="Tn4401b_snp_profiles.txt" />
+            </conditional>
+            <conditional name="struct_profiles_source">
+                <param name="struct_profiles_source_selector" value="history" />
+                <param name="struct_profiles" value="Tn4401b_struct_profiles.txt" />
+            </conditional>
+            <output name="summary" file="output_summary_2.txt" />
+        </test>
+        <test>
+            <param name="reference" value="Tn4401b-1.fasta" />
+            <conditional name="collection_paired">
+                <param name="selector" value="paired" />
+                <param name="forward_input" value="ERR1911133_Tn4401b-1_mapped_subsampled_1.fastq" />
+                <param name="reverse_input" value="ERR1911133_Tn4401b-1_mapped_subsampled_2.fastq" />
+            </conditional>
+            <conditional name="snp_profiles_source">
+                <param name="snp_profiles_source_selector" value="tool_data_table" />
+                <param name="snp_profiles" value="Tn4401b_snp_profiles" />
+            </conditional>
+            <conditional name="struct_profiles_source">
+                <param name="struct_profiles_source_selector" value="tool_data_table" />
+                <param name="struct_profiles" value="Tn4401b_struct_profiles" />
+            </conditional>
             <output name="summary" file="output_summary_2.txt" />
         </test>
     </tests>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test	Fri Jan 10 18:52:22 2020 +0000
@@ -0,0 +1,11 @@
+<?xml version="1.0"?>
+<tables>
+    <table name="tetyper_snp_profiles" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="${__HERE__}/test-data/tetyper_snp_profiles.loc" />
+    </table>
+    <table name="tetyper_struct_profiles" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="${__HERE__}/test-data/tetyper_struct_profiles.loc" />
+    </table>
+</tables>