# HG changeset patch
# User glogobyte
# Date 1603872890 0
# Node ID 766ba9ab0b344efd68d62f55c3c39c98646f6a2f
# Parent  2b09cbf138c8927389aa2ac0b47a72a3e4a1725d
Deleted selected files

diff -r 2b09cbf138c8 -r 766ba9ab0b34 preExample.xml
--- a/preExample.xml	Tue Oct 20 09:41:39 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,59 +0,0 @@
-<tool id="pre_analysis" name="ArmDB: Generation of Pre-miRNA arm reference DB (5p and 3p arms)" version="0.1.0">
-  <description>for each sequence in a file</description>
-  <requirements>
-    <requirement type="package" version="2.28.0">Bedtools</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 $mir_input.genome1.fields.value
-    #else:
-     #set path=$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>
-
-  </help>
-</tool>