changeset 2:fed8439686cb draft

Uploaded

--- a/chewbbaca_createschema.xml	Fri Feb 21 01:09:48 2020 +0000
+++ b/chewbbaca_createschema.xml	Fri Feb 21 01:14:47 2020 +0000
@@ -1,14 +1,19 @@
-<tool id="chewbbaca_prepexternalschema" name="chewBBACA PrepExternalSchema" version="@TOOL_VERSION@+galaxy0">
+<tool id="chewbbaca_createschema" name="chewBBACA CreateSchema" version="@TOOL_VERSION@+galaxy0">
     <description>Adapt an external schema to be used with chewBBACA.</description>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">chewbbaca</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-        chewBBACA.py PrepExternalSchema
+        chewBBACA.py CreateSchema
           --cpu \${GALAXY_SLOTS:-1}
-          -i '${input_files}'
-          #if str( translation_table ) != "":
-            --tbl '${translation_table}'
+          -i '${assemblies}'
+          #if str( prodigal_training_file_source.prodigal_training_file_source_selector ) == 'tool_data_table'
+            --ptf '${prodigal_training_file_source.prodigal_training_file.fields.path}'
+          #elif str( prodigal_training_file_source.prodigal_training_file_source_selector ) == 'history'
+            --ptf '${prodigal_training_file_source.prodigal_training_file}'
+          #end if
+          #if str( cds ) != "":
+            --CDS '${cds}'
           #end if
           --bsr '${bsr}'
           --len '${len}'
@@ -17,9 +22,30 @@
         ]]>
     </command>
     <inputs>
-        <param name="input_files" format="fasta" type="data" multiple="true" label="Schema files (fasta)" />
+        <param name="assemblies" format="fasta" type="data" multiple="true" label="Assembled genomes (fasta)" />
+                <conditional name="prodigal_training_file_source">
+            <param name="prodigal_training_file_source_selector" type="select"
+                   label="Select a Prodigal training file from your history or use one from a tool data table?">
+                <option value="No" selected="true">No Prodigal training file</option>
+                <option value="tool_data_table">Prodigal training file from tool data table</option>
+                <option value="history">Prodigal training file from history</option>
+            </param>
+            <when value="No"/>
+            <when value="tool_data_table">
+                <param name="prodigal_training_file" type="select" format="tabular" label="Prodigal Training File">
+                    <options from_data_table="chewbbaca_prodigal_training_files">
+                        <validator type="no_options" message="No chewBBACA prodigal training files are available" />
+                    </options>
+                </param>
+            </when>
+            <when value="history">
+                <param name="prodigal_training_file" type="data" format="binary"
+                       label="Prodigal training file"
+                       help=""/>
+            </when>
+        </conditional>
         <param name="bsr" type="float" value="0.6" optional="true" label="BSR score" />
-        <param name="min_len" type="integer" min="1" value="100" max="100000" optional="true" label="Minimum length" />
+        <param name="cds" type="data" format="fasta" optional="true" label="Coding sequence file for schema creation (fasta)" />
     </inputs>
     <outputs>
         <data name="schema_zipped" format="zip" label="${tool.name}: on ${on_string}: Schema (zipped)" from_work_dir="schema.tgz"/>