changeset 10:8c00bc7fd8de draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 48c9d7f30655d48c9b46b9ca7a17c454eb54694d

--- a/sam_dump.xml	Wed Jul 12 00:48:56 2017 -0400
+++ b/sam_dump.xml	Fri Nov 17 13:22:37 2017 -0500
@@ -1,4 +1,4 @@
-<tool id="sam_dump" name="Download and Extract Reads in BAM" version="@VERSION@.2">
+<tool id="sam_dump" name="Download and Extract Reads in BAM" version="@VERSION@.3">
     <description>format from NCBI SRA</description>
     <macros>
         <import>sra_macros.xml</import>
@@ -6,7 +6,7 @@
     <expand macro="requirements"/>
     <version_command>sam-dump --version</version_command>
     <command detect_errors="exit_code">
-        <![CDATA[
+<![CDATA[
     #if $input.input_select=="file_list":
       for acc in `cat $input.file_list` ;
       do
@@ -18,8 +18,6 @@
           [ ""\$acc" =~ ^[E|S|D]RR[0-9]{1,}$" ] && (
     #end if
 
-
-
         ## Need to set the home directory to the current working directory,
         ## else the tool tries to write to home/.ncbi and fails when used
         ## with a cluster manager.
@@ -38,19 +36,15 @@
         #end if
         sam-dump --log-level fatal --disable-multithreading
         #if str( $adv.region ) != "":
-            --aligned-region "$adv.region"
+            --aligned-region '$adv.region'
         #end if
         #if str( $adv.matepairDist ) != "":
-            --matepair-distance "$adv.matepairDist"
+            --matepair-distance '$adv.matepairDist'
         #end if
         #if str( $adv.minMapq ) != "":
-            --min-mapq "$adv.minMapq"
+            --min-mapq '$adv.minMapq'
         #end if
-        #if str( $adv.header ) == "yes":
-            --header
-        #else:
-            --no-header
-        #end if
+        --header
         #if str( $adv.alignments ) == "both":
             --unaligned
         #end if
@@ -61,7 +55,7 @@
             --primary
         #end if
         #if $input.input_select == "file":
-            "$input.file"
+            '$input.file'
         #elif $input.input_select == "accession_number":
             "\$acc"
         #elif $input.input_select=="file_list":
@@ -72,9 +66,9 @@
             | samtools view -Sb - 2> /dev/null
         #end if
         #if $input.input_select == "file":
-            > "$output_file"
+            > '$output_file'
         #elif $input.input_select == "accession_number":
-            > "$output_accession" )
+            > '$output_accession' )
         #end if
 
         #if $input.input_select=="file_list":
@@ -86,7 +80,6 @@
         ) ; done
         #end if
 
-
         ]]>
     </command>
     <inputs>
@@ -96,11 +89,6 @@
             <option value="sam">sam</option>
         </param>
         <section name="adv" title="Advanced Options" expanded="False">
-            <param name="header" type="select" value="yes">
-                <label>output header</label>
-                <option value="yes">Yes</option>
-                <option value="no">No</option>
-            </param>
             <expand macro="alignments"/>
             <expand macro="region"/>
             <expand macro="matepairDist"/>
@@ -141,6 +129,7 @@
         </test>
     </tests>
     <help><![CDATA[
+
 **What it does?**
 
 This tool extracts data (in BAM_ format) from the Short Read Archive (SRA) at the National Center for Biotechnology Information (NCBI). It is based on the sam-dump_ utility of the SRA Toolkit.
@@ -191,7 +180,6 @@
 .. _collection: https://galaxyproject.org/tutorials/collections/
 .. _link: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies
 
-
 @SRATOOLS_ATTRRIBUTION@
     ]]></help>
     <expand macro="citation"/>