# HG changeset patch
# User peterjc
# Date 1431684959 14400
# Node ID e98f6bd363ba83f72fce9ac5c09daa3f44656504
# Parent  6119ddccd8a31d2091143df6eb2f6a2c797f7eca
planemo upload for repository https://github.com/peterjc/galaxy_blast/tools/ncbi_blast_plus commit a567843bb239ee8faec72eb7e52f3b5aa3191631

diff -r 6119ddccd8a3 -r e98f6bd363ba tools/ncbi_blast_plus/README.rst
--- a/tools/ncbi_blast_plus/README.rst	Thu Apr 02 04:48:24 2015 -0400
+++ b/tools/ncbi_blast_plus/README.rst	Fri May 15 06:15:59 2015 -0400
@@ -213,6 +213,8 @@
         - Replace ``.extra_files_path`` with ``.files_path`` (internal change,
 	  thanks to Bjoern Gruening and John Chilton).
         - Added "NCBI BLAST+ integrated into Galaxy" preprint citation.
+v0.1.03 - Reorder XML elements (internal change only).
+        - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
 ======= ======================================================================
 
 
@@ -233,10 +235,28 @@
 As of July 2013, development is continuing on a dedicated GitHub repository:
 https://github.com/peterjc/galaxy_blast
 
-For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use
-the following command from the GitHub repository root folder::
+For pushing a release to the test or main "Galaxy Tool Shed", use the following
+Planemo commands (which requires you have set your Tool Shed access details in
+``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
+
+    $ planemo shed_upload --shed_target testtoolshed --check_diff ~/repositories/galaxy_blast/tools/ncbi_blast_plus/
+    ...
+
+or::
 
-    $ tools/ncbi_blast_plus/make_ncbi_blast_plus.sh
+    $ planemo shed_upload --shed_target toolshed --check_diff ~/repositories/galaxy_blast/tools/ncbi_blast_plus/
+    ...
+
+To just build and check the tar ball, use::
+
+    $ planemo shed_upload --tar_only  ~/repositories/galaxy_blast/tools/ncbi_blast_plus/
+    ...
+    $ tar -tzf shed_upload.tar.gz 
+    test-data/blastdb.loc
+    ...
+    tools/ncbi_blast_plus/tool_dependencies.xml
+    $ tar -tzf shed_upload.tar.gz | wc -l
+    117
 
 This simplifies ensuring a consistent set of files is bundled each time,
 including all the relevant test files.
diff -r 6119ddccd8a3 -r e98f6bd363ba tools/ncbi_blast_plus/blastxml_to_tabular.py
--- a/tools/ncbi_blast_plus/blastxml_to_tabular.py	Thu Apr 02 04:48:24 2015 -0400
+++ b/tools/ncbi_blast_plus/blastxml_to_tabular.py	Fri May 15 06:15:59 2015 -0400
@@ -1,9 +1,9 @@
 #!/usr/bin/env python
 """Convert a BLAST XML file to tabular output.
 
-Takes three command line options, input BLAST XML filename, output tabular
-BLAST filename, output format (std for standard 12 columns, or ext for the
-extended 24 columns offered in the BLAST+ wrappers).
+Designed to convert BLAST XML files into tabular BLAST output (either
+std for standard 12 columns, or ext for the extended 25 columns offered
+in the Galaxy BLAST+ wrappers).
 
 The 12 columns output are 'qseqid sseqid pident length mismatch gapopen qstart
 qend sstart send evalue bitscore' or 'std' at the BLAST+ command line, which
diff -r 6119ddccd8a3 -r e98f6bd363ba tools/ncbi_blast_plus/blastxml_to_tabular.xml
--- a/tools/ncbi_blast_plus/blastxml_to_tabular.xml	Thu Apr 02 04:48:24 2015 -0400
+++ b/tools/ncbi_blast_plus/blastxml_to_tabular.xml	Fri May 15 06:15:59 2015 -0400
@@ -1,5 +1,10 @@
-<tool id="blastxml_to_tabular" name="BLAST XML to tabular" version="0.1.04">
+<tool id="blastxml_to_tabular" name="BLAST XML to tabular" version="0.1.05">
     <description>Convert BLAST XML output to tabular</description>
+    <stdio>
+        <!-- Anything other than zero is an error -->
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+    </stdio>
     <version_command interpreter="python">blastxml_to_tabular.py --version</version_command>
     <command interpreter="python">
 blastxml_to_tabular.py -o "$tabular_file"
@@ -11,11 +16,6 @@
 #end if
 #for i in $blastxml_file#"${i}" #end for#
     </command>
-    <stdio>
-        <!-- Anything other than zero is an error -->
-        <exit_code range="1:" />
-        <exit_code range=":-1" />
-    </stdio>
     <inputs>
         <param name="blastxml_file" type="data" format="blastxml" multiple="true" label="BLAST results as XML"/>
         <conditional name="output">
@@ -62,8 +62,6 @@
     <outputs>
         <data name="tabular_file" format="tabular" label="$on_string (as tabular)" />
     </outputs>
-    <requirements>
-    </requirements>
     <tests>
         <test>
             <param name="blastxml_file" value="blastp_four_human_vs_rhodopsin.xml" ftype="blastxml" />
diff -r 6119ddccd8a3 -r e98f6bd363ba tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml
--- a/tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml	Thu Apr 02 04:48:24 2015 -0400
+++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml	Fri May 15 06:15:59 2015 -0400
@@ -1,14 +1,13 @@
-<tool id="ncbi_blastdbcmd_info" name="NCBI BLAST+ database info" version="0.1.02">
+<tool id="ncbi_blastdbcmd_info" name="NCBI BLAST+ database info" version="0.1.03">
     <description>Show BLAST database information from blastdbcmd</description>
     <macros>
         <token name="@BINARY@">blastdbcmd</token>
         <import>ncbi_macros.xml</import>
     </macros>
-    <expand macro="requirements" />
+    <expand macro="preamble" />
     <command>
 blastdbcmd -dbtype $db_opts.db_type -db "${db_opts.database.fields.path}" -info -out "$info"
     </command>
-    <expand macro="stdio" />
     <inputs>
         <expand macro="input_conditional_choose_db_type" />
     </inputs>
diff -r 6119ddccd8a3 -r e98f6bd363ba tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml	Thu Apr 02 04:48:24 2015 -0400
+++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml	Fri May 15 06:15:59 2015 -0400
@@ -1,10 +1,10 @@
-<tool id="ncbi_blastdbcmd_wrapper" name="NCBI BLAST+ blastdbcmd entry(s)" version="0.1.02">
+<tool id="ncbi_blastdbcmd_wrapper" name="NCBI BLAST+ blastdbcmd entry(s)" version="0.1.03">
     <description>Extract sequence(s) from BLAST database</description>
     <macros>
         <token name="@BINARY@">blastdbcmd</token>
         <import>ncbi_macros.xml</import>
     </macros>
-    <expand macro="requirements" />
+    <expand macro="preamble" />
     <command>
 ## The command is a Cheetah template which allows some Python based syntax.
 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
@@ -47,7 +47,6 @@
 | sed 's/>\(lcl|\|gnl|BL_ORD_ID|[0-9]* \)/>/1' > "$seq"
 #end if
     </command>
-    <expand macro="stdio" />
     <inputs>
         <expand macro="input_conditional_choose_db_type" />
         <conditional name="id_opts">
diff -r 6119ddccd8a3 -r e98f6bd363ba tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml	Thu Apr 02 04:48:24 2015 -0400
+++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml	Fri May 15 06:15:59 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.1.02">
+<tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.1.03">
     <description>Search nucleotide database with nucleotide query sequence(s)</description>
     <!-- If job splitting is enabled, break up the query file into parts -->
     <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" merge_outputs="output1"></parallelism>
@@ -6,7 +6,7 @@
         <token name="@BINARY@">blastn</token>
         <import>ncbi_macros.xml</import>
     </macros>
-    <expand macro="requirements" />
+    <expand macro="preamble" />
     <command>
 ## The command is a Cheetah template which allows some Python based syntax.
 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
@@ -31,14 +31,9 @@
 ## End of advanced options:
 #end if
     </command>
-
-    <expand macro="stdio" />
-
     <inputs>
         <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> 
-
         <expand macro="input_conditional_nucleotide_db" />
-
         <param name="blast_type" type="select" display="radio" label="Type of BLAST">
             <option value="megablast">megablast - Traditional megablast used to find very similar (e.g., intraspecies or closely related species) sequences</option>
             <option value="blastn">blastn - Traditional BLASTN requiring an exact match of 11, for somewhat similar sequences</option>
diff -r 6119ddccd8a3 -r e98f6bd363ba tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml	Thu Apr 02 04:48:24 2015 -0400
+++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml	Fri May 15 06:15:59 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="ncbi_blastp_wrapper" name="NCBI BLAST+ blastp" version="0.1.02">
+<tool id="ncbi_blastp_wrapper" name="NCBI BLAST+ blastp" version="0.1.03">
     <description>Search protein database with protein query sequence(s)</description>
     <!-- If job splitting is enabled, break up the query file into parts -->
     <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" merge_outputs="output1" />
@@ -6,7 +6,7 @@
         <token name="@BINARY@">blastp</token>
         <import>ncbi_macros.xml</import>
     </macros>
-    <expand macro="requirements" />
+    <expand macro="preamble" />
     <command>
 ## The command is a Cheetah template which allows some Python based syntax.
 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
@@ -29,9 +29,6 @@
 ## End of advanced options:
 #end if
     </command>
-
-    <expand macro="stdio" />
-
     <inputs>
         <param name="query" type="data" format="fasta" label="Protein query sequence(s)"/> 
 
diff -r 6119ddccd8a3 -r e98f6bd363ba tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml	Thu Apr 02 04:48:24 2015 -0400
+++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml	Fri May 15 06:15:59 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="ncbi_blastx_wrapper" name="NCBI BLAST+ blastx" version="0.1.02">
+<tool id="ncbi_blastx_wrapper" name="NCBI BLAST+ blastx" version="0.1.03">
     <description>Search protein database with translated nucleotide query sequence(s)</description>
     <!-- If job splitting is enabled, break up the query file into parts -->
     <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" merge_outputs="output1"></parallelism>
@@ -6,7 +6,7 @@
         <token name="@BINARY@">blastx</token>
         <import>ncbi_macros.xml</import>
     </macros>
-    <expand macro="requirements" />
+    <expand macro="preamble" />
     <command>
 ## The command is a Cheetah template which allows some Python based syntax.
 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
@@ -30,9 +30,6 @@
 ## End of advanced options:
 #end if
     </command>
-
-    <expand macro="stdio" />
-
     <inputs>
         <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> 
 
diff -r 6119ddccd8a3 -r e98f6bd363ba tools/ncbi_blast_plus/ncbi_convert2blastmask_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_convert2blastmask_wrapper.xml	Thu Apr 02 04:48:24 2015 -0400
+++ b/tools/ncbi_blast_plus/ncbi_convert2blastmask_wrapper.xml	Fri May 15 06:15:59 2015 -0400
@@ -1,10 +1,10 @@
-<tool id="ncbi_convert2blastmask_wrapper" name="NCBI BLAST+ convert2blastmask" version="0.1.02">
+<tool id="ncbi_convert2blastmask_wrapper" name="NCBI BLAST+ convert2blastmask" version="0.1.03">
     <description>Convert masking information in lower-case masked FASTA input to file formats suitable for makeblastdb</description>
     <macros>
         <token name="@BINARY@">convert2blastmask</token>
         <import>ncbi_macros.xml</import>
     </macros>
-    <expand macro="requirements" />
+    <expand macro="preamble" />
     <command>
 ## The command is a Cheetah template which allows some Python based syntax.
 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
@@ -16,7 +16,6 @@
 -out "$outfile"
 -outfmt $outformat
     </command>
-    <expand macro="stdio" />
     <inputs>
         <param name="infile" type="data" format="fasta" label="masked FASTA file"/> 
         <param name="masking_algorithm" type="select" label="Used masking algorithm">
diff -r 6119ddccd8a3 -r e98f6bd363ba tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml	Thu Apr 02 04:48:24 2015 -0400
+++ b/tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml	Fri May 15 06:15:59 2015 -0400
@@ -1,11 +1,11 @@
-<tool id="ncbi_dustmasker_wrapper" name="NCBI BLAST+ dustmasker" version="0.1.02">
+<tool id="ncbi_dustmasker_wrapper" name="NCBI BLAST+ dustmasker" version="0.1.03">
     <!-- dustmasker wrapper from Edward Kirton and Nicola Soranzo -->
     <description>masks low complexity regions</description>
     <macros>
         <token name="@BINARY@">dustmasker</token>
         <import>ncbi_macros.xml</import>
     </macros>
-    <expand macro="requirements" />
+    <expand macro="preamble" />
     <command>
 ## The command is a Cheetah template which allows some Python based syntax.
 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
@@ -20,7 +20,6 @@
 -out "$outfile"
 -window $window -level $level -linker $linker -outfmt $outformat
     </command>
-    <expand macro="stdio" />
     <inputs>
         <expand macro="input_conditional_nucleotide_db" />
         <param name="window" type="integer" value="64" label="DUST window length" />
diff -r 6119ddccd8a3 -r e98f6bd363ba tools/ncbi_blast_plus/ncbi_macros.xml
--- a/tools/ncbi_blast_plus/ncbi_macros.xml	Thu Apr 02 04:48:24 2015 -0400
+++ b/tools/ncbi_blast_plus/ncbi_macros.xml	Fri May 15 06:15:59 2015 -0400
@@ -1,9 +1,18 @@
 <macros>
-    <xml name="requirements">
+    <xml name="preamble">
         <requirements>
             <requirement type="binary">@BINARY@</requirement>
             <requirement type="package" version="2.2.30">blast+</requirement>
         </requirements>
+        <stdio>
+            <!-- Anything other than zero is an error -->
+            <exit_code range="1:" />
+            <!-- Might see negative return codes for Unix signals via Python subprocess -->
+            <exit_code range=":-1" />
+            <!-- In case the return code has not been set properly check stderr too -->
+            <regex match="Error:" />
+            <regex match="Exception:" />
+        </stdio>
         <version_command>@BINARY@ -version</version_command>
     </xml>
     <xml name="output_change_format">
@@ -116,17 +125,6 @@
             <option value="PAM30">PAM30</option>
         </param>
     </xml>
-    <xml name="stdio">
-        <stdio>
-            <!-- Anything other than zero is an error -->
-            <exit_code range="1:" />
-            <!-- Might see negative return codes for Unix signals via Python subprocess -->
-            <exit_code range=":-1" />
-            <!-- In case the return code has not been set properly check stderr too -->
-            <regex match="Error:" />
-            <regex match="Exception:" />
-        </stdio>
-    </xml>
     <xml name="input_query_gencode">
         <param name="query_gencode" type="select" label="Query genetic code">
             <!-- See http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi for details -->
diff -r 6119ddccd8a3 -r e98f6bd363ba tools/ncbi_blast_plus/ncbi_makeblastdb.xml
--- a/tools/ncbi_blast_plus/ncbi_makeblastdb.xml	Thu Apr 02 04:48:24 2015 -0400
+++ b/tools/ncbi_blast_plus/ncbi_makeblastdb.xml	Fri May 15 06:15:59 2015 -0400
@@ -1,10 +1,10 @@
-<tool id="ncbi_makeblastdb" name="NCBI BLAST+ makeblastdb" version="0.1.02">
+<tool id="ncbi_makeblastdb" name="NCBI BLAST+ makeblastdb" version="0.1.03">
     <description>Make BLAST database</description>
     <macros>
         <token name="@BINARY@">makeblastdb</token>
         <import>ncbi_macros.xml</import>
     </macros>
-    <expand macro="requirements" />
+    <expand macro="preamble" />
     <command interpreter="python">check_no_duplicates.py
 ##First check for duplicates (since BLAST+ 2.2.28 fails to do so)
 ##and abort (via the ampersand ampersand trick) if any are found.
@@ -47,7 +47,6 @@
 ## Capture the stdout log information to the primary file (plain text):
 &gt; "$outfile"
     </command>
-    <expand macro="stdio" />
     <inputs>
         <param name="dbtype" type="select" display="radio" label="Molecule type of input">
             <option value="prot">protein</option>
diff -r 6119ddccd8a3 -r e98f6bd363ba tools/ncbi_blast_plus/ncbi_makeprofiledb.xml
--- a/tools/ncbi_blast_plus/ncbi_makeprofiledb.xml	Thu Apr 02 04:48:24 2015 -0400
+++ b/tools/ncbi_blast_plus/ncbi_makeprofiledb.xml	Fri May 15 06:15:59 2015 -0400
@@ -1,10 +1,10 @@
-<tool id="ncbi_makeprofiledb" name="NCBI BLAST+ makeprofiledb" version="0.1.02">
+<tool id="ncbi_makeprofiledb" name="NCBI BLAST+ makeprofiledb" version="0.1.03">
     <description>Make profile database</description>
     <macros>
         <token name="@BINARY@">makeprofiledb</token>
         <import>ncbi_macros.xml</import>
     </macros>
-    <expand macro="requirements" />
+    <expand macro="preamble" />
     <command>
 ##Unlike makeblastdb, makeprofiledb needs directory to exist already:
 mkdir -p $outfile.files_path &amp;&amp;
@@ -34,7 +34,13 @@
 
 -logfile "$outfile"
     </command>
-    <expand macro="stdio" />
+    <configfiles>
+        <configfile name="infiles">
+#for $infile in $input_file
+${infile}
+#end for
+        </configfile>
+    </configfiles>
     <inputs>
         <param name="input_file" type="data" multiple="true" optional="false" format="pssm-asn1"
 	       label="Input PSSM files(s)"
@@ -75,13 +81,6 @@
             label="Observation threshold"            
             help="Exclude domains with with maximum number of independent observations below this threshold" />
     </inputs>
-    <configfiles>
-        <configfile name="infiles">
-#for $infile in $input_file
-${infile}
-#end for
-        </configfile>
-    </configfiles>
     <outputs>
         <data name="outfile" format="blastdbd" label="RPS database from ${on_string}" />
     </outputs>
diff -r 6119ddccd8a3 -r e98f6bd363ba tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml	Thu Apr 02 04:48:24 2015 -0400
+++ b/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml	Fri May 15 06:15:59 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="ncbi_rpsblast_wrapper" name="NCBI BLAST+ rpsblast" version="0.1.02">
+<tool id="ncbi_rpsblast_wrapper" name="NCBI BLAST+ rpsblast" version="0.1.03">
     <description>Search protein domain database (PSSMs) with protein query sequence(s)</description>
     <!-- If job splitting is enabled, break up the query file into parts -->
     <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" merge_outputs="output1" />
@@ -6,7 +6,7 @@
         <token name="@BINARY@">deltablast</token>
         <import>ncbi_macros.xml</import>
     </macros>
-    <expand macro="requirements" />
+    <expand macro="preamble" />
     <command>
 ## The command is a Cheetah template which allows some Python based syntax.
 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
@@ -27,9 +27,6 @@
 ## End of advanced options:
 #end if
     </command>
-
-    <expand macro="stdio" />
-
     <inputs>
         <param name="query" type="data" format="fasta" label="Protein query sequence(s)"/> 
 
diff -r 6119ddccd8a3 -r e98f6bd363ba tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml	Thu Apr 02 04:48:24 2015 -0400
+++ b/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml	Fri May 15 06:15:59 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="ncbi_rpstblastn_wrapper" name="NCBI BLAST+ rpstblastn" version="0.1.02">
+<tool id="ncbi_rpstblastn_wrapper" name="NCBI BLAST+ rpstblastn" version="0.1.03">
     <description>Search protein domain database (PSSMs) with translated nucleotide query sequence(s)</description>
     <!-- If job splitting is enabled, break up the query file into parts -->
     <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" merge_outputs="output1"></parallelism>
@@ -6,7 +6,7 @@
         <token name="@BINARY@">rpstblastn</token>
         <import>ncbi_macros.xml</import>
     </macros>
-    <expand macro="requirements" />
+    <expand macro="preamble" />
     <command>
 ## The command is a Cheetah template which allows some Python based syntax.
 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
@@ -28,7 +28,6 @@
 ## End of advanced options:
 #end if
     </command>
-    <expand macro="stdio" />
     <inputs>
         <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> 
 
diff -r 6119ddccd8a3 -r e98f6bd363ba tools/ncbi_blast_plus/ncbi_segmasker_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_segmasker_wrapper.xml	Thu Apr 02 04:48:24 2015 -0400
+++ b/tools/ncbi_blast_plus/ncbi_segmasker_wrapper.xml	Fri May 15 06:15:59 2015 -0400
@@ -1,10 +1,10 @@
-<tool id="ncbi_segmasker_wrapper" name="NCBI BLAST+ segmasker" version="0.1.02">
+<tool id="ncbi_segmasker_wrapper" name="NCBI BLAST+ segmasker" version="0.1.03">
     <description>low-complexity regions in protein sequences</description>
     <macros>
         <token name="@BINARY@">segmasker</token>
         <import>ncbi_macros.xml</import>
     </macros>
-    <expand macro="requirements" />
+    <expand macro="preamble" />
     <command>
 ## The command is a Cheetah template which allows some Python based syntax.
 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
@@ -22,7 +22,6 @@
 -hicut $hicut
 -outfmt $outformat
     </command>
-    <expand macro="stdio" />
     <inputs>
         <expand macro="input_conditional_protein_db" />
         <param name="window" type="integer" value="12" label="SEG window length" help="(-window)" />
diff -r 6119ddccd8a3 -r e98f6bd363ba tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml	Thu Apr 02 04:48:24 2015 -0400
+++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml	Fri May 15 06:15:59 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="0.1.02">
+<tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="0.1.03">
     <description>Search translated nucleotide database with protein query sequence(s)</description>
     <!-- If job splitting is enabled, break up the query file into parts -->
     <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" merge_outputs="output1"></parallelism>
@@ -6,7 +6,7 @@
         <token name="@BINARY@">tblastn</token>
         <import>ncbi_macros.xml</import>
     </macros>
-    <expand macro="requirements" />
+    <expand macro="preamble" />
     <command>
 ## The command is a Cheetah template which allows some Python based syntax.
 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
@@ -30,9 +30,6 @@
 ## End of advanced options:
 #end if
     </command>
-
-    <expand macro="stdio" />
-
     <inputs>
         <param name="query" type="data" format="fasta" label="Protein query sequence(s)"/> 
 
diff -r 6119ddccd8a3 -r e98f6bd363ba tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml	Thu Apr 02 04:48:24 2015 -0400
+++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml	Fri May 15 06:15:59 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="ncbi_tblastx_wrapper" name="NCBI BLAST+ tblastx" version="0.1.02">
+<tool id="ncbi_tblastx_wrapper" name="NCBI BLAST+ tblastx" version="0.1.03">
     <description>Search translated nucleotide database with translated nucleotide query sequence(s)</description>
     <!-- If job splitting is enabled, break up the query file into parts -->
     <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" merge_outputs="output1"></parallelism>
@@ -6,7 +6,7 @@
         <token name="@BINARY@">tblastx</token>
         <import>ncbi_macros.xml</import>
     </macros>
-    <expand macro="requirements" />
+    <expand macro="preamble" />
     <command>
 ## The command is a Cheetah template which allows some Python based syntax.
 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
@@ -29,9 +29,6 @@
 ## End of advanced options:
 #end if
     </command>
-
-    <expand macro="stdio" />
-
     <inputs>
         <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/>