--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sam_dump.xml	Wed Nov 04 06:57:32 2015 -0500
@@ -0,0 +1,117 @@
+<tool id="sam_dump" name="Extract reads" version="1.2.4">
+    <description>in SAM or BAM format from NCBI SRA.</description>
+    <macros>
+        <import>sra_macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command>
+        <![CDATA[
+        ## 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. 
+        export HOME=\$PWD;
+        vdb-config --restore-defaults;
+        vdb-config -s "/repository/user/main/public/root=\$PWD";
+        ## Do not use prefetch if region is specified, to avoid downloading
+        ## the complete sra file.
+        #if ( str( $adv.region ) == "" ):
+            ASCP_PATH=`which ascp`;
+            ASCP_KEY=`dirname \$ASCP_PATH`/asperaweb_id_dsa.openssh;
+            prefetch --ascp-path "\$ASCP_PATH|\$ASCP_KEY" "$input.accession";
+        ##Duplicate vdb-config, in case settings changed between prefetch and
+        ##dump command.
+        #end if
+        vdb-config -s "/repository/user/main/public/root=\$PWD";
+        sam-dump --log-level fatal --disable-multithreading
+        #if str( $adv.region ) != "":
+        --aligned-region "$adv.region"
+        #end if
+        #if str( $adv.matepairDist ) != "":
+        --matepair-distance "$adv.matepairDist"
+        #end if
+        #if str( $adv.minMapq ) != "":
+        --min-mapq "$adv.minMapq"
+        #end if
+        #if str( $adv.header ) == "yes":
+        --header
+        #else:
+        --no-header
+        #end if
+        #if str( $adv.alignments ) == "both":
+        --unaligned
+        #end if
+        #if str( $adv.alignments ) == "unaligned":
+        --unaligned-spots-only
+        #end if
+        #if (str( $adv.primary ) == "yes") and (str ( $adv.alignments != "unaligned") ):
+        --primary
+        #end if
+        #if $input.input_select == "file":
+        "$input.file"
+        #elif $input.input_select == "accession_number":
+        "$input.accession"
+        #end if
+        #if str( $outputformat ) == "bam":
+            | samtools view -Sb - 2> /dev/null
+        #end if
+        #if $input.input_select == "file":
+        > "$output_file"
+        #elif $input.input_select == "accession_number":
+        > "$output_accession"
+        #end if
+        ]]>
+    </command>
+    <version_string>sam-dump --version</version_string>
+    <inputs>
+        <expand macro="input_conditional"/>
+        <param name="outputformat" type="select" label="select output format">
+            <option value="bam">bam</option>
+            <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"/>
+            <param name="primary" type="select" value="no">
+                <label>only primary aligments</label>
+                <option value="no">No</option>
+                <option value="yes">Yes</option>
+            </param>
+            <expand macro="minMapq"></expand>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="output_accession" format="bam" label="${input.accession}.${outputformat}">
+            <filter>input['input_select'] == "accession_number"</filter>
+            <change_format>
+                <when input="outputformat" value="sam" format="sam"/>
+            </change_format>
+        </data>
+        <data name="output_file" format="bam" label="${input.file.name}.${outputformat}">
+            <filter>input['input_select'] == "file"</filter>
+            <change_format>
+                <when input="outputformat" value="sam" format="sam"/>
+            </change_format>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_select" value="accession_number"/>
+            <param name="accession" value="SRR925743"/>
+            <param name="outputformat" value="sam"/>
+            <param name="region" value="17:41243452-41277500"/>
+            <output name="output_accession" file="sam_dump_result.sam" ftype="sam"/>
+        </test>
+    </tests>
+    <help>
+        This tool extracts reads from sra archives using sam-dump.
+        The sam-dump program is developed at NCBI, and is available at
+        http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software.
+        @SRATOOLS_ATTRRIBUTION@
+    </help>
+</tool>