ydeng/autoBIGS.galaxy
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Separated information CSV output

Browse Source
This commit is contained in:
Harrison Deng 2025-02-21 22:18:13 +00:00
parent 52bd3ac07d
commit 5042d0d5fa
1 changed files with 11 additions and 8 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

19
autobigs-cli.xml
View File

@ -14,9 +14,9 @@
<command detect_errors="exit_code"><![CDATA[ <command detect_errors="exit_code"><![CDATA[
#if $mode['operation'] == "info": #if $mode['operation'] == "info":
#if $select_info['retrieved'] == "schemas": #if $select_info['retrieved'] == "schemas":
autoBIGS info $selected_schema --csv $info_out autoBIGS info $selected_schema --csv $info_db_out
#else if $select_info['retrieved'] == "databases": #else if $select_info['retrieved'] == "databases":
autoBIGS info --retrieve-bigsdbs --csv $info_out autoBIGS info --retrieve-bigsdbs --csv $info_schemes_out
#end if #end if
#else if $mode['operation'] == "st": #else if $mode['operation'] == "st":
autoBIGS st "$fastas" "$seqdefdb" $schema "$mlst_profiles_output" $stop_on_fail autoBIGS st "$fastas" "$seqdefdb" $schema "$mlst_profiles_output" $stop_on_fail
@ -31,12 +31,12 @@
<when value="info"> <when value="info">
<conditional name="select_info"> <conditional name="select_info">
<param name="retrieved" label="Schemas or Database List" type="select"> <param name="retrieved" label="Schemas or Database List" type="select">
<option value="schemas">Available Schemas for Database</option> <option value="schemes">Available Schemas for Database</option>
<option value="databases">Available Databases</option> <option value="databases">Available Databases</option>
</param> </param>
<when value="schemas"> <when value="schemes">
<repeat name="schemas_list" title="Schemas" min="1"> <repeat name="schemes_list" title="Schemes" min="1">
<param name="selected_schema" argument="--retrieve-bigsdb-schemas" label="Retrieve schemas for" type="text"/> <param name="selected_db" argument="--retrieve-bigsdb-schemas" label="Database to retrieve schemes from" type="text"/>
</repeat> </repeat>
</when> </when>
<when value="databases"> <when value="databases">
@ -56,9 +56,12 @@
<data name="mlst_profiles_output" label="${tool.name} on ${on_string}" format="csv"> <data name="mlst_profiles_output" label="${tool.name} on ${on_string}" format="csv">
<filter>mode['operation'] == "st"</filter> <filter>mode['operation'] == "st"</filter>
</data> </data>
<data name="info_out" label="${tool.name} supported Databases" format="csv"> <data name="info_db_out" label="${tool.name} supported Databases" format="csv">
<filter>mode['operation'] == "info" and select_info['retrieved'] == 'databases'</filter> <filter>mode['operation'] == "info" and select_info['retrieved'] == 'databases'</filter>
</data> </data>
<data name="info_schemes_out" label="${tool.name} supported Databases" format="csv">
<filter>mode['operation'] == "info" and select_info['retrieved'] == 'schemes'</filter>
</data>
</outputs> </outputs>
<tests> <tests>
<test expect_num_outputs="1"> <test expect_num_outputs="1">
@ -71,7 +74,7 @@
<test expect_num_outputs="1"> <test expect_num_outputs="1">
<param name="operation" value="info" /> <param name="operation" value="info" />
<param name="retrieved" value="databases" /> <param name="retrieved" value="databases" />
<output name="info_out"> <output name="info_db_out">
<assert_contents> <assert_contents>
<has_text text="BIGSdb Names,Source"/> <has_text text="BIGSdb Names,Source"/>
<has_text text="pubmlst_bordetella_seqdef,https://bigsdb.pasteur.fr/api"/> <has_text text="pubmlst_bordetella_seqdef,https://bigsdb.pasteur.fr/api"/>