diff tools/ncbi_blast_plus/ncbi_convert2blastmask_wrapper.xml @ 22:6f386c5dc4fb draft

v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates

--- a/tools/ncbi_blast_plus/ncbi_convert2blastmask_wrapper.xml	Wed Apr 19 05:27:19 2017 -0400
+++ b/tools/ncbi_blast_plus/ncbi_convert2blastmask_wrapper.xml	Mon Sep 18 06:21:27 2017 -0400
@@ -5,36 +5,36 @@
         <import>ncbi_macros.xml</import>
     </macros>
     <expand macro="preamble" />
-    <command>
+    <command detect_errors="aggressive">
 ## The command is a Cheetah template which allows some Python based syntax.
 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
 convert2blastmask
--in $infile
--masking_algorithm "$masking_algorithm"
--masking_options "$masking_options"
+-in '$infile'
+-masking_algorithm '$masking_algorithm'
+-masking_options '$masking_options'
 $parse_seqids
--out "$outfile"
+-out '$outfile'
 -outfmt $outformat
     </command>
     <inputs>
-        <param name="infile" type="data" format="fasta" label="masked FASTA file"/> 
-        <param name="masking_algorithm" type="select" label="Used masking algorithm">
+        <param name="infile" argument="-in" type="data" format="fasta" label="Masked FASTA file"/>
+        <param argument="-masking_algorithm" type="select" label="Used masking algorithm">
             <option value="dust">DUST</option>
             <option value="seg" selected="true">SEG</option>
             <option value="windowmasker">windowmasker</option>
             <option value="repeat">repeat</option>
             <option value="other">other</option>
         </param>
-        <param name="masking_options" type="text" value="" size="20" label="Masking algorithm options to create the masked input" 
-            help ="free text to describe the options used to create the masking files. (-masking_options)">
+        <param argument="-masking_options" type="text" value="" size="20" label="Masking algorithm options to create the masked input"
+            help ="Free text to describe the options used to create the masking files">
             <sanitizer invalid_char="">
                 <valid initial="string.printable" />
             </sanitizer>
         </param>
-        <param name="parse_seqids" type="boolean" truevalue="-parse_seqids" falsevalue="" checked="true" label="Parse Seq-ids in FASTA input" help="(-parse_seqids)" />
-        <param name="outformat" type="select" label="Output format">
+        <param argument="-parse_seqids" type="boolean" truevalue="-parse_seqids" falsevalue="" checked="true" label="Parse Seq-ids in FASTA input" help="(-parse_seqids)" />
+        <param name="outformat" argument="-outfmt" type="select" label="Output format">
             <option value="maskinfo_asn1_bin">maskinfo ASN.1 binary</option>
-            <option value="maskinfo_asn1_text" selected="True">maskinfo ASN.1 text</option>
+            <option value="maskinfo_asn1_text" selected="true">maskinfo ASN.1 text</option>
             <option value="maskinfo_xml">maskinfo_xml</option>
         </param>
     </inputs>
@@ -42,9 +42,9 @@
         <data name="outfile" format="maskinfo-asn1" label="SEG Masked File">
             <change_format>
                 <when input="outformat" value="maskinfo_asn1_bin" format="maskinfo-asn1-binary" />
-		<!--
+                <!--
                 <when input="outformat" value="maskinfo_asn1_text" format="maskinfo-asn1" />
-		-->
+                -->
                 <when input="outformat" value="maskinfo_xml" format="xml" />
             </change_format>
         </data>
@@ -54,7 +54,7 @@
             <param name="infile" value="four_human_proteins_masked.fasta" ftype="fasta" />
             <param name="masking_algorithm" value="seg" />
             <param name="masking_options" value="window=12; locut=2.2; hicut=2.5" />
-            <param name="parse_seqids" value="True" />
+            <param name="parse_seqids" value="true" />
             <param name="outformat" value="maskinfo_asn1_bin" />
             <output name="outfile" file="convert2blastmask_four_human_masked.maskinfo-asn1-binary" />
         </test>
@@ -62,7 +62,7 @@
             <param name="infile" value="four_human_proteins_masked.fasta" ftype="fasta" />
             <param name="masking_algorithm" value="seg" />
             <param name="masking_options" value="window=12; locut=2.2; hicut=2.5" />
-            <param name="parse_seqids" value="True" />
+            <param name="parse_seqids" value="true" />
             <param name="outformat" value="maskinfo_asn1_text" />
             <output name="outfile" file="convert2blastmask_four_human_masked.maskinfo-asn1" />
         </test>