# HG changeset patch
# User glogobyte
# Date 1638706866 0
# Node ID bb3a4324ecd0b9e3215f7376b85c6da279ee0f58
# Parent  66dd837b4e5c2ab88eba0714766d62623e7b613e
Uploaded

diff -r 66dd837b4e5c -r bb3a4324ecd0 isoread.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/isoread.xml	Sun Dec 05 12:21:06 2021 +0000
@@ -0,0 +1,80 @@
+<tool id="ArmDB" name="ArmDB: Generation of Pre-miRNA arm reference DB (5p and 3p arms)" version="0.1.0">
+  <requirements>
+    <requirement type="package" version="2.28.0">Bedtools</requirement>
+     <requirement type="package" version="3.7.4">python</requirement>
+  </requirements>
+  <command>
+    #if $mir_input.analysis == "1":
+     #set path=$mir_input.genome1.fields.dbkey
+     python $__tool_directory__/pre_mirbase.py -pos $positions -tool_dir $__tool_directory__ -gff3 "$path" -gen $mir_input.genome1.fields.value
+    #end if    
+    #if $mir_input.analysis == "2":
+     #set path=$mir_input.genome2.fields.value
+     python $__tool_directory__/pre_mirgene.py -pos $positions -tool_dir $__tool_directory__ -sym "$path"
+    #end if
+  </command>
+  <inputs>
+   <conditional name="mir_input">
+    <param name="analysis" type="select" label="Choose reference Mir database" help="Choose which database prefer to be used.">
+      <option value="1" selected="true">MirBase</option>
+      <option value="2">MirGene</option>
+    </param>
+    <when value="1">
+        <param name="genome1" type="select" label="Choose organism" help="If your genome coordinates of interest is not listed, contact the Galaxy team">
+          <options from_data_table="mirbase" />
+        </param> 
+    </when>
+    <when value="2">
+      <param name="genome2" type="select" label="Choose organism" help="If your genome coordinates of interest is not listed, contact the" >
+        <options from_data_table="mirgene" />
+      </param>
+    </when>
+   </conditional>
+   <param name="positions" type="integer" min="0" max="8" value="1" label="Custom Arm length" help="Choose how many nucleotides you want to extend the 5p and 3p mature sequences to create the refernce arms" />
+  </inputs>
+  <outputs>
+    <data name="shifted_gff1" format="txt" label="Custom Bed file" from_work_dir="$__tool_directory__/shifted_mirnas.bed">
+         <filter>mir_input['analysis']== "1" </filter>
+    </data>
+    <data name="normal_gff1" format="fasta" label="Official Bed file" from_work_dir="$__tool_directory__/original_mirnas.bed" >
+       	 <filter>mir_input['analysis']== "1" </filter>
+    </data>
+    <data name="custom reference genome1" format="fasta" label="Custom reference arms" from_work_dir="$__tool_directory__/new_ref.fa" >
+       	 <filter>mir_input['analysis']== "1" </filter>
+    </data>
+
+    <data name="shifted_gff" format="txt" label="Mature and star miRNA sequences" from_work_dir="$__tool_directory__/shifted_mirnas.bed">
+       	 <filter>mir_input['analysis']== "2" </filter>
+    </data>
+    <data name="normal_gff" format="fasta" label="Primary transcripts with flanks" from_work_dir="$__tool_directory__/original_mirnas.bed" >
+         <filter>mir_input['analysis']== "2" </filter>
+    </data>
+    <data name="custom reference genome" format="fasta" label="Custom reference arms" from_work_dir="$__tool_directory__/new_ref.fa" >
+    	 <filter>mir_input['analysis']== "2" </filter>
+    </data>
+
+  </outputs>
+  <help><![CDATA[
+.. class:: infomark
+
+**What it does**
+
+-----
+
+**Inputs**
+
+- Genome coordinates in General Feature Format (GFF3) or FASTA files of RefSeq miRNAs
+
+ArmDB takes genome coordinates (GFF3) files from MirBase or FASTA files from MirGene as input. GFF3 files and FASTA files are downloaded directly from the databases.
+
+.. image:: armdb.png
+
+**Outputs**
+
+- ArmDB generates FASTA files containing the custom reference arms that are produced with the user-defined nucleotides extension of the RefSeq sequences (up to 8 nt)
+
+ ]]></help>
+  <citations>
+     <citation type="doi">10.3390/cancers13225663</citation>
+  </citations>
+</tool>