diff dbkit_create.xml @ 0:8b48a608f1df draft

"planemo upload commit b68cb41b1884703c4f1574b65a6408d7d0cca321"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dbkit_create.xml	Tue Mar 23 23:06:15 2021 +0000
@@ -0,0 +1,73 @@
+<tool id="ffindex_dbkit_create" name="DBKit Create" version="0.1.1" license="MIT" profile="20.01">
+    <description>database</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+    mkdir -p inputs &&
+    #for item in $inputs
+        ln -s '${item}' 'inputs/${item.element_identifier}' &&
+    #end for
+    dbkit_create.py
+        -l '$input'
+        -p 'inputs'
+        -o '$index'
+        -d '$database'
+        -g '$log'
+        -il '$advanced.idlength'
+        -ic '$advanced.idcase'
+        -ie '$advanced.idextension'
+    ]]>    </command>
+    <inputs>
+        <param name="input" type="data" format="tabular" label="List of Identifiers" help="Specify a list containing all entry identifiers to be downloaded." />
+        <param name="inputs" type="data" format="txt" multiple="true" label="Specify your datasets" help="The datasets that you want to convert into an ffindex." />
+        <conditional name="advanced">
+            <param name="type" type="select" label="Identifier Formatting Options" help="">
+                <option value="true">Yes, I want to format my identifiers</option>
+                <option value="false">No formatting</option>
+            </param>
+            <when value="true">
+                <param name="idextension" type="text" optional="true" label="Identifier Extensions" help="Specify the extension of the identifier" />
+                <param name="idlength" type="integer" label="Identifier Length" value="0" min="0" max="20" help="Specify the length of the identifier (disable=0)." />
+                <param name="idcase" type="select" label="Identifier Case" display="radio" help="Choose to format the identifier by changing its case (optional).">
+                    <option value="">Unformatted</option>
+                    <option value="lower">Lower</option>
+                    <option value="upper">Upper</option>
+                </param>
+            </when>
+            <when value="false">
+                <param name="idextension" type="hidden" value="" />
+                <param name="idlength" type="hidden" value="0" />
+                <param name="idcase" type="hidden" value="" />
+            </when>
+        </conditional>
+        <expand macro="logfile" />
+    </inputs>
+    <outputs>
+        <data name="index" format="ffindex" label="DBKit Index" />
+        <data name="database" format="ffdata" label="DBKit Database" />
+        <data format="txt" name="log" label="DBKit Log">
+            <filter>logfile</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="create/sequences.tabular" ftype="tabular" />
+            <param name="inputs" value="create/NP_000282.1.hhr,create/NP_000290.2.hhr,create/NP_000548.2.hhr,create/NP_000836.2.hhr" />
+            <conditional name="advanced">
+                <param name="type" value="false" />
+            </conditional>
+            <output name="index" file="create/sequences.ffindex" ftype="ffindex" />
+            <output name="database" file="create/sequences.ffdata" ftype="ffdata" />
+        </test>
+    </tests>
+    <help><![CDATA[
+
+**What it does**
+
+This database creation tool downloads entries from an external resource and creates a datasets with all its contents. Additionally an index file is
+generated indicating the start and size of every entry within the database file. The tool can also operate on collections.
+    ]]>    </help>
+    <expand macro="citations" />
+</tool>