diff search.xml @ 0:854be3d51221 draft

Uploaded 20171204

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/search.xml	Mon Dec 04 16:05:45 2017 -0500
@@ -0,0 +1,69 @@
+<?xml version="1.0"?>
+<tool name="Search" id="srase_search" version="1.0.0">
+    <description>your sequences in the big SRA data lake</description>
+    <requirements>
+        <requirement type="package" version="2.7.10">python</requirement>
+        <requirement type="package" version="2.18.4">requests</requirement>
+        <requirement type="package" version="0.9.7">requests-futures</requirement>
+    </requirements>
+    <command detect_errors="exit_code">
+<![CDATA[
+    python '$__tool_directory__/search.py'
+    
+    #if $search_condition.sequences:
+        --sequences '${search_condition.sequences}'
+    #end if
+    --search ${search_condition.search}
+    
+    #if $search_condition.search is 0:
+        #set file_paths = ','.join( [ str( $f ) for $f in $search_condition.txtfiles ] )
+        #if $file_paths is not 'None':
+            --files '${file_paths}'
+            #set file_names = ','.join( [ str( $f.name ) for $f in $search_condition.txtfiles ] )
+                --names '${file_names}'
+        #end if
+    #elif $search_condition.search is 1:
+        #set file_paths = ','.join( [ str( $f ) for $f in $search_condition.fastafiles ] )
+        #if $file_paths is not 'None':
+            --files '${file_paths}'
+            #set file_names = ','.join( [ str( $f.name ) for $f in $search_condition.fastafiles ] )
+                --names '${file_names}'
+        #end if
+        --exact ${search_condition.exact}
+    #end if
+
+    --sthreshold '${sthreshold}'
+    --output '${output}'
+]]>
+    </command>
+    <inputs>
+        <conditional name="search_condition">
+            <param name="search" type="select" label="Search mode" help="Select a search mode between normal (slower but returns an optimal solution) and fast (faster but it is heuristic)">
+                <option value="0" selected="true">Normal</option>
+                <option value="1">Fast</option>
+            </param>
+            <when value="0">
+                <param format="txt" name="txtfiles" type="data" label="Select sequences" multiple="true" optional="true" help="Select one or more txt files containing a sequence. A single file can contain more sequences, one for each row. Every file will represent a query to the Sequence Read Archive Search Engine that will return a list of accession numbers in which your sequences occur on." />
+                <param name="sequences" type="text" area="True" size="5x25" label="Manually insert sequence" optional="true" help="Optionally you can put a list of sequences (one for each row) in this text field." />
+            </when>
+            <when value="1">
+                <param format="fasta" name="fastafiles" type="data" label="Select fasta files" multiple="true" optional="false" help="Select one or more fasta files containing sequences. These files represent queries to the Sequence Read Archive Search Engine that will return a list of accession numbers in which your sequences occur on." />
+                <param name="exact" type="boolean" truevalue="1" falsevalue="0" checked="False" label="Use exact algorithm" help="" />
+            </when>
+        </conditional>
+        <param name="sthreshold" size="3" type="float" value="0.5" min="0.0" max="1.0" label="Threshold applied to the search algorithm" />
+    </inputs>
+    <outputs>
+        <data name="output" format="txt" label="${tool.name} on ${on_string}: SRA-SE Search Result" />
+    </outputs>
+
+    <help><![CDATA[
+Authors: Fabio Cumbo, Robert S. Harris, Chen Sun, Paul Medvedev, and Anton Nekrutenko
+
+Help section
+    ]]></help>
+
+    <citations>
+        <citation type="doi">10.1101/090464</citation>
+    </citations>
+</tool>