diff data_manager/homer_genome_preparse.xml @ 0:5d2e5fddec81 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/homer_genome_preparse.xml	Sun Aug 08 10:57:48 2021 +0000
@@ -0,0 +1,60 @@
+<tool id="homer_genome_preparse_data_manager" name="Homer genome preparse" tool_type="manage_data" version="@IDX_VERSION@" profile="20.05">
+    <requirements>
+        <requirement type="package" version="@IDX_VERSION@">homer</requirement>
+        <requirement type="package" version="3.9">python</requirement>
+    </requirements>
+    <macros>
+        <token name="@IDX_VERSION@">4.11</token>
+    </macros>
+    <command detect_errors="exit_code"><![CDATA[
+        python '$__tool_directory__/homer_genome_preparse.py'
+        '${out_file}'
+        --fasta_filename '${all_fasta_source.fields.path}'
+        --fasta_dbkey '${all_fasta_source.fields.dbkey}'
+        --fasta_description '${all_fasta_source.fields.name}'
+        ${mask}
+        --size '${size}'
+        --index_version '@IDX_VERSION@'
+        --data_table_name homer_preparse
+    ]]></command>
+    <inputs>
+        <param name="all_fasta_source" type="select" label="Source FASTA Sequence">
+            <options from_data_table="all_fasta"/>
+        </param>
+        <param name="sequence_name" type="text" value="" label="Name of sequence" />
+        <param name="sequence_id" type="text" value="" label="ID for sequence" />
+        <param name="mask" type="boolean" truevalue="--mask" falsevalue="" checked="False" label="mask repeats/lower case sequence" />
+        <param name="size" type="integer" value="200" min="0" label="fragment size to use for motif finding" />
+    </inputs>
+    <outputs>
+        <data name="out_file" format="data_manager_json"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="all_fasta_source" value="phiX174"/>
+            <output name="out_file" >
+                <assert_contents>
+                    <has_text text="{&quot;data_tables&quot;: {&quot;homer_preparse&quot;: [{&quot;dbkey&quot;: &quot;phiX174&quot;, &quot;mask&quot;: &quot;False&quot;, &quot;name&quot;: &quot;phiX174 (200bp)&quot;, &quot;path&quot;: &quot;phiX174_200&quot;, &quot;path_fasta&quot;:" />
+                    <has_text text="test-data/phiX174.fasta&quot;, &quot;size&quot;: &quot;200&quot;, &quot;value&quot;: &quot;phiX174_200&quot;, &quot;version&quot;: &quot;4.11&quot;}]}}" />
+                </assert_contents>                
+            </output>
+        </test>
+        <test>
+            <param name="all_fasta_source" value="phiX174"/>
+            <param name="mask" value="True"/>
+            <param name="size" value="100"/>
+            <output name="out_file" >
+                <assert_contents>
+                    <has_text text="{&quot;data_tables&quot;: {&quot;homer_preparse&quot;: [{&quot;dbkey&quot;: &quot;phiX174&quot;, &quot;mask&quot;: &quot;True&quot;, &quot;name&quot;: &quot;phiX174 masked (100bp)&quot;, &quot;path&quot;: &quot;phiX174r_100&quot;, &quot;path_fasta&quot;:" />
+                    <has_text text="test-data/phiX174.fasta&quot;, &quot;size&quot;: &quot;100&quot;, &quot;value&quot;: &quot;phiX174r_100&quot;, &quot;version&quot;: &quot;4.11&quot;}]}}" />
+                </assert_contents>                
+            </output>
+        </test>
+    </tests>
+
+    <help>
+.. class:: infomark
+
+**Notice:** If you leave name, description, or id blank, it will be generated automatically.
+    </help>
+</tool>