diff sra_macros.xml @ 7:c7620aa7e1f0 draft

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

--- a/sra_macros.xml	Wed Mar 22 05:23:31 2017 -0400
+++ b/sra_macros.xml	Wed May 10 10:45:41 2017 -0400
@@ -1,19 +1,28 @@
 <macros>
-    <token name="@VERSION@">2.8.0</token>
+    <token name="@VERSION@">2.8.1</token>
     <macro name="requirements">
         <requirements>
-            <requirement type="package" version="2.8.0">sra-tools</requirement>
+            <requirement type="package" version="2.8.1">sra-tools</requirement>
         </requirements>
     </macro>
     <macro name="input_conditional">
         <conditional name="input">
             <param name="input_select" type="select" label="select input type">
                 <option value="accession_number">SRR accession</option>
+                <option value="file_list">List of SRA accession, one per line</option>
                 <option value="file">SRA archive in current history</option>
-                <option value="file_list">List of SRA accession, one per line</option>
             </param>
             <when value="accession_number">
-                <param name="accession" type="text" label="SRR accession" help="Must start with SRR,DRR or ERR, e.g. SRR925743 , ERR343809"/>
+                <param name="accession" type="text" label="Accession" help="Must start with SRR,DRR or ERR, e.g. SRR925743 ,ERR343809">
+                    <sanitizer>
+                        <valid initial="string.printable">
+                            <remove value=" "/>
+                        </valid>
+                        <mapping initial="none">
+                            <add source=" " target=""/>
+                        </mapping>
+                    </sanitizer>
+                </param>
             </when>
             <when value="file">
                 <param format="sra" name="file" type="data" label="sra archive"/>
@@ -24,39 +33,45 @@
         </conditional>
     </macro>
     <macro name="alignments">
-        <param name="alignments" type="select" value="both">
-            <label>aligned or unaligned reads</label>
+        <param name="alignments" type="select" value="both" label="Output aligned or unaligned reads" help="Output reads according to their alignment status." argument="--aligned and --unaligned">
             <option value="both">both</option>
             <option value="aligned">aligned only</option>
             <option value="unaligned">unaligned only</option>
         </param>
     </macro>
     <macro name="minMapq">
-        <param name="minMapq" type="integer" min="0" max="42" label="minimum mapping quality" optional="true"/>
+        <param name="minMapq" type="integer" min="0" max="42" label="Minimum mapping quality" optional="true" help="Minimum mapping quality an alignment has to have, to be dumped." argument="--min-mapq"/>
     </macro>
     <macro name="region">
         <param format="text" name="region" type="text" label="aligned region" optional="true"
-               help="Filter by position on genome. Can be either accession.version (ex: NC_000001.10), chromosome name (ex:chr1 or 1) or 1-based coordinates (ex: chr1:1-101)."/>
+               help="Filter by position on genome. Can be either accession.version (ex: NC_000001.10), chromosome name (ex:chr1 or 1) or 1-based coordinates (ex: chr1:1-101)." argument="--aligned-region"/>
     </macro>
     <macro name="matepairDist">
         <param name="matepairDist" type="text" label="mate-pair distance (from-to|unknown)" optional="true"
-               help="Filter by distance between matepairs. Use unknown to find matepairs split between the references. Use from-to (inclusive) to limit matepair distance on the same reference"/>
+               help="Filter by distance between matepairs. Use unknown to find matepairs split between the references. Use from-to (inclusive) to limit matepair distance on the same reference" argument="--matepair-distance"/>
     </macro>
     <macro name="citation">
         <citations>
             <citation type="doi">10.1093/nar/gkq1019</citation>
         </citations>
     </macro>
-    <token name="@SRATOOLS_ATTRRIBUTION@">
-        Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies.
+    <token name="@ACCESSION_LIST_HOWTO@">
+-----
 
-        Galaxy tool wrapper originally written by Matt Shirley (mdshw5 at gmail.com).
+**How to generate accession lists**
 
-        Wrapper modified by Philip Mabon ( philip.mabon at phac-aspc.gc.ca ).
+ 1. Go to **SRA Run Selector** by clicking this link_
+ 2. Find the study you are interested in by typing a search term within the **Search** box. This can be a word (e.g., *mitochondria*) or an accession you have gotten from a paper (e.g., *SRR1582967*). 
+ 3. Once you click on the study of interest you will see the number of datasets in this study within the **Related SRA data** box
+ 4. Click on the Runs number
+ 5. On the page that would open you will see **Accession List** button
+ 6. Clicking of this button will produce a file that you will need to upload into Galaxy and use as the input to this tool.
+    </token>
 
-        Tool dependencies, clean-up and bug-fixes by Marius van den Beek (m.vandenbeek at gmail.com).
-
-        For support and bug reports contact Matt Shirley or Marius van den Beek or go to https://github.com/galaxyproject/tools-iuc.
-
+    <token name="@SRATOOLS_ATTRRIBUTION@">
+Galaxy tool wrapper originally written by Matt Shirley (mdshw5 at gmail.com).
+Wrapper modified by Philip Mabon ( philip.mabon at phac-aspc.gc.ca ).
+Tool dependencies, clean-up and bug-fixes by Marius van den Beek (m.vandenbeek at gmail.com).
+For support and bug reports contact Matt Shirley or Marius van den Beek or go to https://github.com/galaxyproject/tools-iuc.
     </token>
 </macros>