Mercurial > repos > greg > vsnp_build_tables

changeset 10:14384fd2a7e2 draft

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Uploaded
author greg
date Thu, 29 Jul 2021 15:02:47 +0000
parents f641e52353e8
children be32fbc45ae8
files .shed.yml static/images/._table_description.png vsnp_build_tables.xml
diffstat 3 files changed, 20 insertions(+), 9 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/.shed.yml	Thu Jul 29 15:02:47 2021 +0000
@@ -0,0 +1,11 @@
+name: vsnp_build_tables
+owner: greg
+description: |
+  Contains a tool that produces Excel spreadsheets from outputs produced by the vsnp_get_snps tool.
+homepage_url: https://github.com/USDA-VS/vSNP
+long_description: |
+  Contains a tool that produces Excel spreadsheets from outputs produced by the vsnp_get_snps tool.
+remote_repository_url: https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_build_tables
+type: unrestricted
+categories:
+  - Sequence Analysis
Binary file static/images/._table_description.png has changed
--- a/vsnp_build_tables.xml	Thu Jul 29 13:52:48 2021 +0000
+++ b/vsnp_build_tables.xml	Thu Jul 29 15:02:47 2021 +0000
@@ -22,17 +22,17 @@
     mkdir $input_json_dir &&
     #for $i in $input_type_cond.input_avg_mq_json_collection:
         #set file_name = $i.file_name
-        #set identifier = re.sub('[^\s\w\-]', '_', str($i.element_identifier))
+        #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier))
         ln -s '$file_name' '$input_json_avg_mq_dir/$identifier' &&
     #end for
     #for $i in $input_type_cond.input_snps_json_collection:
         #set file_name = $i.file_name
-        #set identifier = re.sub('[^\s\w\-]', '_', str($i.element_identifier))
+        #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier))
         ln -s '$file_name' '$input_json_dir/$identifier' &&
     #end for
     #for $i in $input_type_cond.input_newick_collection:
         #set file_name = $i.file_name
-        #set identifier = re.sub('[^\s\w\-]', '_', str($i.element_identifier))
+        #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier))
         ln -s '$file_name' '$input_newick_dir/$identifier' &&
     #end for
 #end if
@@ -139,12 +139,12 @@
             </param>
             <param name="gbk_param" value="no"/>
             <output_collection name="excel" type="list" count="6">
-                <element name="Mbovis-01D6_snps_newick_cascade_table" file="Mbovis-01D6_cascade_table.xlsx" ftype="xlsx" compare="sim_size"/>
-                <element name="Mbovis-01D6_snps_newick_sort_table" file="Mbovis-01D6_sort_table.xlsx" ftype="xlsx" compare="sim_size"/>
-                <element name="Mbovis-01D_snps_newick_cascade_table" file="Mbovis-01D_cascade_table.xlsx" ftype="xlsx" compare="sim_size"/>
-                <element name="Mbovis-01D_snps_newick_sort_table" file="Mbovis-01D_sort_table.xlsx" ftype="xlsx" compare="sim_size"/>
-                <element name="Mbovis-01_snps_newick_cascade_table" file="Mbovis-01_cascade_table.xlsx" ftype="xlsx" compare="sim_size"/>
-                <element name="Mbovis-01_snps_newick_sort_table" file="Mbovis-01_sort_table.xlsx" ftype="xlsx" compare="sim_size"/>
+                <element name="Mbovis-01D6_snps_cascade_table" file="Mbovis-01D6_cascade_table.xlsx" ftype="xlsx" compare="sim_size"/>
+                <element name="Mbovis-01D6_snps_sort_table" file="Mbovis-01D6_sort_table.xlsx" ftype="xlsx" compare="sim_size"/>
+                <element name="Mbovis-01D_snps_cascade_table" file="Mbovis-01D_cascade_table.xlsx" ftype="xlsx" compare="sim_size"/>
+                <element name="Mbovis-01D_snps_sort_table" file="Mbovis-01D_sort_table.xlsx" ftype="xlsx" compare="sim_size"/>
+                <element name="Mbovis-01_snps_cascade_table" file="Mbovis-01_cascade_table.xlsx" ftype="xlsx" compare="sim_size"/>
+                <element name="Mbovis-01_snps_sort_table" file="Mbovis-01_sort_table.xlsx" ftype="xlsx" compare="sim_size"/>
             </output_collection>
         </test>
     </tests>