diff sra_pileup.xml @ 7:c7620aa7e1f0 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1

--- a/sra_pileup.xml	Wed Mar 22 05:23:31 2017 -0400
+++ b/sra_pileup.xml	Wed May 10 10:45:41 2017 -0400
@@ -1,5 +1,5 @@
-<tool id="sra_pileup" name="Generate pileup format" version="@VERSION@">
-    <description>from NCBI sra.</description>
+<tool id="sra_pileup" name="Generate pileup format" version="@VERSION@.2">
+    <description>from NCBI sra</description>
     <macros>
         <import>sra_macros.xml</import>
     </macros>
@@ -7,6 +7,11 @@
     <version_command>sra-pileup --version</version_command>
     <command detect_errors="exit_code">
         <![CDATA[
+
+        #if $input.input_select=="accession_number":
+            acc="${input.accession}" &&
+        #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.
@@ -16,7 +21,7 @@
         #if ( str( $adv.region ) == "" ):
             ASCP_PATH=`command -v ascp` &&
             ASCP_KEY=`dirname \$ASCP_PATH`/asperaweb_id_dsa.openssh || true &&
-            prefetch -X 200G --ascp-path "\$ASCP_PATH|\$ASCP_KEY" "$input.accession" &&
+            prefetch -X 200G --ascp-path "\$ASCP_PATH|\$ASCP_KEY" "\$acc" &&
             ## Duplicate vdb-config, in case settings changed between prefetch and
             ## sra-pileup command.
             vdb-config -s "/repository/user/main/public/root=\$PWD" &&
@@ -31,7 +36,7 @@
         #if $input.input_select == "file":
             "$input.file" > "$output_file"
         #elif $input.input_select == "accession_number":
-            "$input.accession" > "$output_accession"
+            "\$acc" > "$output_accession"
         #elif $input.input_select == "text":
             `cat "$input.text"` > "$output_text"
         #end if
@@ -48,7 +53,16 @@
                 <param format="sra" name="file" type="data" label="sra archive"/>
             </when>
             <when value="accession_number">
-                <param format="text" name="accession" type="text" label="SRR accession" help="Must start with SRR, e.g. SRR925743"/>
+                <param format="text" name="accession" type="text" label="SRR accession" help="Must start with SRR, e.g. SRR925743">
+                    <sanitizer>
+                        <valid initial="string.printable">
+                            <remove value=" "/>
+                        </valid>
+                        <mapping initial="none">
+                            <add source=" " target=""/>
+                        </mapping>
+                    </sanitizer>
+                </param>
             </when>
             <when value="text">
                 <param format="txt" name="text" type="data" label="text file"/>
@@ -60,13 +74,13 @@
         </section>
     </inputs>
     <outputs>
-        <data format="pileup" name="output_accession" label="${input.accession}.pileup">
+        <data format="pileup" name="output_accession" label="${input.accession} (sra-pileup)">
             <filter>input['input_select'] == "accession_number"</filter>
         </data>
-        <data format="pileup" name="output_file" label="${input.file.name}.pileup">
+        <data format="pileup" name="output_file" label="${input.file.name} (sra-pileup)">
             <filter>input['input_select'] == "file"</filter>
         </data>
-        <data format="pileup" name="output_text" label="${input.text.name}.pileup">
+        <data format="pileup" name="output_text" label="${input.text.name} (sra-pileup)">
             <filter>input['input_select'] == "text"</filter>
         </data>
     </outputs>
@@ -79,10 +93,14 @@
         </test>
     </tests>
     <help>
-        This tool produces pileup format from sra archives using sra-pileup.
-        The sra-pileup program is developed at NCBI, and is available at
-        http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software.
-        @SRATOOLS_ATTRRIBUTION@
+ <![CDATA[
+
+This tool produces pileup format from sra archives using sra-pileup.
+The sra-pileup program is developed at NCBI, and is available at
+http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software.
+@SRATOOLS_ATTRRIBUTION@
+
+]]>
     </help>
     <expand macro="citation"/>
 </tool>