--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sam_dump.xml	Thu Feb 02 18:11:05 2023 -0500
@@ -0,0 +1,127 @@
+<tool id="sam_dump" name="Download and Extract Reads in BAM" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>format from NCBI SRA</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="edam_ontology"/>
+    <expand macro="bio_tools"/>
+    <expand macro="requirements"/>
+    <version_command>sam-dump --version | tr -d $'\n'</version_command>
+    <command detect_errors="exit_code"><![CDATA[
+        @COPY_CONFIGFILE@
+        @SET_ACCESSIONS@
+
+        ## Do not use prefetch if region is specified, to avoid downloading
+        ## the complete sra file.
+
+        #if $input.input_select == "sra_file":
+            sam-dump --log-level fatal  --accession '\$acc'
+        #else:
+            #if ( str( $adv.region ) == "" ):
+                prefetch -X 200000000 "\$acc" &&
+            #end if
+            sam-dump --log-level fatal --disable-multithreading
+        #end if
+
+        #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
+        --header
+        #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
+        "\$acc"
+
+        #if str( $outputformat ) == "bam":
+            | samtools view -Sb - 2> /dev/null > "\$acc.bam"
+        #elif str( $outputformat ) == "sam":
+            > "\$acc.sam"
+        #end if
+        
+        #if $input.input_select != "sra_file":
+            ); done;
+        #end if
+        echo "Done with all accessions."
+        ]]>
+    </command>
+    <expand macro="configfile_hack"/>
+    <inputs>
+        <expand macro="input_conditional"/>
+        <param name="outputformat" type="select" display="radio" label="select output format" help="In vast majority of cases you want to download data in bam format. It is more compact and is accepted by all downstream tools.">
+            <option value="bam">bam</option>
+            <option value="sam">sam</option>
+        </param>
+        <section name="adv" title="Advanced Options" expanded="False">
+            <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>
+        <collection name="output_collection" type="list" label="sam-dump: Downloaded SAM/BAM data">
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.bam" directory="." ext='bam'/>
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.sam" directory="." ext='sam'/>
+        </collection>
+    </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_collection name="output_collection" type="list" count="1">
+                <element name="SRR925743" file="SRR925743_sam_dump_result.sam" compare="contains" ftype="sam"/>
+            </output_collection>
+        </test>
+        <test>
+            <param name="input_select" value="accession_number"/>
+            <param name="accession" value="SRR925743,SRR522874"/>
+            <param name="outputformat" value="sam"/>
+            <param name="region" value="17:41243452-41277500"/>
+            <output_collection name="output_collection" type="list" count="2">
+                <element name="SRR522874" file="SRR522874_sam_dump_result.sam" compare="contains" ftype="sam"/>
+                <element name="SRR925743" file="SRR925743_sam_dump_result.sam" compare="contains" ftype="sam"/>
+            </output_collection>
+        </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 and returns a collection of NGS data containing one file for each accession number provided.
+
+
+@HOW_TO_USE_IT@
+
+@ACCESSION_LIST_HOWTO@
+
+-----
+
+.. _sam-dump: https://github.com/ncbi/sra-tools
+.. _BAM: https://samtools.github.io/hts-specs/SAMv1.pdf
+.. _collection: https://galaxyproject.org/tutorials/collections/
+.. _link: https://trace.ncbi.nlm.nih.gov/Traces/index.html?view=run_browser&display=reads
+
+@SRATOOLS_ATTRRIBUTION@
+    ]]></help>
+    <expand macro="citation"/>
+</tool>