diff macros.xml @ 17:33d070cbe5ee draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863"

--- a/macros.xml	Tue Dec 03 22:39:30 2019 +0000
+++ b/macros.xml	Mon Mar 22 13:20:30 2021 +0000
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@VERSION@">0.9.29</token>
+    <token name="@VERSION@">2.0.8</token>
 
     <xml name="requirements">
         <requirements>
@@ -9,14 +9,12 @@
 
     <xml name="stdio">
         <stdio>
-            <exit_code range=":-1" level="fatal"  description="Error occurred. Please check Tool Standard Error" />
-            <exit_code range="1:" level="fatal"  description="Error occurred. Please check Tool Standard Error" />
-            <regex match="Failed to allocate sufficient memory." source="stderr" level="fatal_oom" />
+            <regex match="Failed to allocate" source="stderr" level="fatal_oom" />
         </stdio>
     </xml>
 
     <xml name="version_command">
-        <version_command>diamond version</version_command>
+        <version_command>diamond version | cut -d" " -f 3</version_command>
     </xml>
 
     <xml name="output_type_macro">
@@ -30,7 +28,7 @@
                 <option value="102">Taxonomic classification</option>
             </param>
             <when value="0"/>
-	    <when value="5"/>
+            <when value="5"/>
             <when value="6">
                 <param name="fields" type="select" label="Tabular fields" help="" multiple="true">
                     <option value="qseqid" selected="true">Query Seq - id</option>
@@ -52,12 +50,13 @@
                     <option value="send" selected="true">End of alignment in subject</option>
                     <option value="qseq">Aligned part of query sequence</option>
                     <option value="sseq">Aligned part of subject sequence</option>
+                    <option value="qseq_translated">Translation of the aligned part of query sequence</option>
                     <option value="evalue" selected="true">Expect value</option>
                     <option value="bitscore" selected="true">Bit score</option>
                     <option value="score">Raw score</option>
                     <option value="qframe">Query frame</option>
                     <option value="btop">Blast traceback operations(BTOP)</option>
-                    <option value="staxids">unique Subject Taxonomy ID(s), separated by a ';' (in numerical order)</option>
+                    <option value="scovhsp">Subject coverage per HSP</option>
                     <option value="stitle">Subject Title</option>
                     <option value="salltitles">All Subject Title(s)</option>
                     <option value="qcovhsp">Query Coverage Per HSP</option>
@@ -67,13 +66,15 @@
                     <option value="qqual">Query quality values for the aligned part of the query</option>
                     <option value="full_qqual">Query quality values</option>
                     <option value="qstrand">Query strand</option>
+                    <option value="cigar">Cigar</option>
+                    <yield/>
                 </param>
             </when>
             <when value="100">
                 <param argument="--salltitles" type="boolean" truevalue="--salltitles" falsevalue="" checked="true" label="Include full subject titles in DAA file?" help=""/>
                 <param argument="--sallseqid" type="boolean" truevalue="--sallseqid" falsevalue="" checked="true" label="Include all subject ids in DAA file?" help=""/>
             </when>
-	    <when value="101">
+            <when value="101">
                 <param argument="--salltitles" type="boolean" truevalue="--salltitles" falsevalue="" checked="true" label="Include full subject titles in DAA file?" help=""/>
                 <param argument="--sallseqid" type="boolean" truevalue="--sallseqid" falsevalue="" checked="true" label="Include all subject ids in DAA file?" help=""/>
             </when>
@@ -97,6 +98,14 @@
         </conditional>
     </xml>
 
+    <xml name="block_size_low_sens">
+        <param name="block_size" argument="--block-size" type="float" value="2" label="Block size in billions of sequence letters to be processed at a time" help="" />
+    </xml>
+
+    <xml name="block_size_hi_sens">
+        <param name="block_size" argument="--block-size" type="float" value="0.4" label="Block size in billions of sequence letters to be processed at a time" help="" />
+    </xml>
+
     <xml name="citations">
         <citations>
             <citation type="doi">10.1038/nmeth.3176</citation>
@@ -115,7 +124,7 @@
             <filter>output["outfmt"] == "6"</filter>
         </data>
         <!-- for daa diamond appends the .daa extension -> hence from_work_dir -->
-	<data format="daa" name="daa_output" label="${tool.name} on ${on_string}" from_work_dir="output.daa">
+        <data format="daa" name="daa_output" label="${tool.name} on ${on_string}" from_work_dir="output.daa">
             <filter>output["outfmt"] == "100"</filter>
         </data>
         <data format="sam" name="sam_output" label="${tool.name} on ${on_string}">
@@ -153,6 +162,6 @@
             --max-target-seqs '$hit_filter.max_target_seqs'
         #else:
             --top '$hit_filter.top'
-	#end if
+        #end if
     </token>
 </macros>