# HG changeset patch
# User peterjc
# Date 1495107633 14400
# Node ID 771b554bc85de15af93e6b206ca8054d6f6a9fb7
# Parent  c5f20ca77de2d50a4c7f133485bbdd869c7e9785
planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 39737c01a51469d0cf9920273de6c151ba84048d-dirty

diff -r c5f20ca77de2 -r 771b554bc85d tools/ncbi_blast_plus/README.rst
--- a/tools/ncbi_blast_plus/README.rst	Wed Apr 26 06:47:08 2017 -0400
+++ b/tools/ncbi_blast_plus/README.rst	Thu May 18 07:40:33 2017 -0400
@@ -213,7 +213,7 @@
           table definitions in Galaxy's ``tool_data_table_conf.xml`` file,
           setup via ``tool-data/tool_data_table_conf.xml.sample``
         - Replace ``.extra_files_path`` with ``.files_path`` (internal change,
-	  thanks to Bjoern Gruening and John Chilton).
+          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).
@@ -233,11 +233,11 @@
           (contribution from Gildas Le Corguillé and Emma Prudent).
         - Minor XML and Python style changes (internal change only).
         - Set ``allow_duplicate_entries="False"`` in sample configuration file
-	  ``tool_data_table_conf.xml``.
+          ``tool_data_table_conf.xml``.
         - Fix identifers with pipes in ``blastdbcmd`` wrapper (Devon Ryan).
 v0.2.00 - Updated for NCBI BLAST+ 2.5.0, where GI numbers are less visible,
           tabular output changes with `-parse_deflines`, and percentage
-	  identifies are now given to 3dp rather than 2dp.
+          identifies are now given to 3dp rather than 2dp.
         - Depends on ``package_blast_plus_2_5_0`` in ToolShed, or BioConda.
         - ``blastxml_to_tabular`` now also gives percentage idenity to 3dp.
         - Removed never-used binary and Python module dependency declarations
diff -r c5f20ca77de2 -r 771b554bc85d tools/ncbi_blast_plus/blastxml_to_tabular.xml
--- a/tools/ncbi_blast_plus/blastxml_to_tabular.xml	Wed Apr 26 06:47:08 2017 -0400
+++ b/tools/ncbi_blast_plus/blastxml_to_tabular.xml	Thu May 18 07:40:33 2017 -0400
@@ -18,7 +18,7 @@
         <param name="blastxml_file" type="data" format="blastxml" multiple="true" label="BLAST results as XML"/>
         <conditional name="output">
           <param name="out_format" type="select" label="Output format">
-            <option value="std" selected="True">Tabular (standard 12 columns)</option>
+            <option value="std" selected="true">Tabular (standard 12 columns)</option>
             <option value="ext">Tabular (extended 25 columns)</option>
             <option value="cols">Tabular (select columns to output)</option>
           </param>
diff -r c5f20ca77de2 -r 771b554bc85d tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml	Wed Apr 26 06:47:08 2017 -0400
+++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml	Thu May 18 07:40:33 2017 -0400
@@ -5,7 +5,7 @@
         <import>ncbi_macros.xml</import>
     </macros>
     <expand macro="preamble" />
-    <command detect_errors="aggressive" strict="True">
+    <command detect_errors="aggressive" strict="true">
 ## The command is a Cheetah template which allows some Python based syntax.
 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
 blastdbcmd -dbtype $db_opts.db_type -db "${db_opts.database.fields.path}"
@@ -58,7 +58,7 @@
                 <param name="entries" type="data" format="txt,tabular" label="Sequence identifier(s)" help="Plain text file with one ID per line (i.e. single column tabular file)"/>
             </when>
             <when value="prompt">
-                <param name="entries" type="text" label="Sequence identifier(s)" help="Comma or new line separated list." optional="False" area="True" size="10x30"/>
+                <param name="entries" type="text" label="Sequence identifier(s)" help="Comma or new line separated list." optional="false" area="true" size="10x30"/>
             </when>
         </conditional>
         <param name="outfmt" type="select" label="Output format">
diff -r c5f20ca77de2 -r 771b554bc85d tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml	Wed Apr 26 06:47:08 2017 -0400
+++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml	Thu May 18 07:40:33 2017 -0400
@@ -72,11 +72,11 @@
             <param name="blast_type" value="blastp" />
             <param name="out_format" value="5" />
             <param name="adv_opts_selector" value="advanced" />
-            <param name="filter_query" value="False" />
+            <param name="filter_query" value="false" />
             <param name="matrix" value="BLOSUM62" />
             <param name="max_hits" value="0" />
             <param name="word_size" value="0" />
-            <param name="parse_deflines" value="True" />
+            <param name="parse_deflines" value="true" />
             <param name="qcov_hsp_perc" value="25" />
             <output name="output1" file="blastp_four_human_vs_rhodopsin.xml" ftype="blastxml" />
         </test>
@@ -89,11 +89,11 @@
             <param name="blast_type" value="blastp" />
             <param name="out_format" value="6" />
             <param name="adv_opts_selector" value="advanced" />
-            <param name="filter_query" value="False" />
+            <param name="filter_query" value="false" />
             <param name="matrix" value="BLOSUM62" />
             <param name="max_hits" value="0" />
             <param name="word_size" value="0" />
-            <param name="parse_deflines" value="True" />
+            <param name="parse_deflines" value="true" />
             <param name="qcov_hsp_perc" value="25" />
             <output name="output1" file="blastp_four_human_vs_rhodopsin.tabular" ftype="tabular" />
         </test>
@@ -106,11 +106,11 @@
             <param name="blast_type" value="blastp" />
             <param name="out_format" value="ext" />
             <param name="adv_opts_selector" value="advanced" />
-            <param name="filter_query" value="False" />
+            <param name="filter_query" value="false" />
             <param name="matrix" value="BLOSUM62" />
             <param name="max_hits" value="0" />
             <param name="word_size" value="0" />
-            <param name="parse_deflines" value="True" />
+            <param name="parse_deflines" value="true" />
             <param name="qcov_hsp_perc" value="25" />
             <output name="output1" file="blastp_four_human_vs_rhodopsin_ext.tabular" ftype="tabular" />
         </test>
diff -r c5f20ca77de2 -r 771b554bc85d tools/ncbi_blast_plus/ncbi_convert2blastmask_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_convert2blastmask_wrapper.xml	Wed Apr 26 06:47:08 2017 -0400
+++ b/tools/ncbi_blast_plus/ncbi_convert2blastmask_wrapper.xml	Thu May 18 07:40:33 2017 -0400
@@ -34,7 +34,7 @@
         <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">
             <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>
diff -r c5f20ca77de2 -r 771b554bc85d tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml	Wed Apr 26 06:47:08 2017 -0400
+++ b/tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml	Thu May 18 07:40:33 2017 -0400
@@ -40,9 +40,9 @@
             <change_format>
                 <when input="outformat" value="fasta" format="fasta" />
                 <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>
diff -r c5f20ca77de2 -r 771b554bc85d tools/ncbi_blast_plus/ncbi_macros.xml
--- a/tools/ncbi_blast_plus/ncbi_macros.xml	Wed Apr 26 06:47:08 2017 -0400
+++ b/tools/ncbi_blast_plus/ncbi_macros.xml	Thu May 18 07:40:33 2017 -0400
@@ -25,7 +25,7 @@
         <conditional name="output">
             <param name="out_format" type="select" label="Output format">
                 <option value="6">Tabular (standard 12 columns)</option>
-                <option value="ext" selected="True">Tabular (extended 25 columns)</option>
+                <option value="ext" selected="true">Tabular (extended 25 columns)</option>
                 <option value="cols">Tabular (select which columns)</option>
                 <option value="5">BLAST XML</option>
                 <option value="0">Pairwise text</option>
@@ -123,7 +123,7 @@
     <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 -->
-            <option value="1" selected="True">1. Standard</option>
+            <option value="1" selected="true">1. Standard</option>
             <option value="2">2. Vertebrate Mitochondrial</option>
             <option value="3">3. Yeast Mitochondrial</option>
             <option value="4">4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>
@@ -146,7 +146,7 @@
     <xml name="input_db_gencode">
         <param name="db_gencode" type="select" label="Database/subject genetic code">
             <!-- See http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi for details -->
-            <option value="1" selected="True">1. Standard</option>
+            <option value="1" selected="true">1. Standard</option>
             <option value="2">2. Vertebrate Mitochondrial</option>
             <option value="3">3. Yeast Mitochondrial</option>
             <option value="4">4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>
@@ -169,7 +169,7 @@
     <xml name="input_conditional_nucleotide_db">
         <conditional name="db_opts">
             <param name="db_opts_selector" type="select" label="Subject database/sequences">
-              <option value="db" selected="True">Locally installed BLAST database</option>
+              <option value="db" selected="true">Locally installed BLAST database</option>
               <option value="histdb">BLAST database from your history</option>
               <option value="file">FASTA file from your history (see warning note below)</option>
             </param>
@@ -195,7 +195,7 @@
     <xml name="input_conditional_protein_db">
         <conditional name="db_opts">
             <param name="db_opts_selector" type="select" label="Subject database/sequences">
-              <option value="db" selected="True">Locally installed BLAST database</option>
+              <option value="db" selected="true">Locally installed BLAST database</option>
               <option value="histdb">BLAST database from your history</option>
               <option value="file">FASTA file from your history (see warning note below)</option>
             </param>
@@ -221,7 +221,7 @@
     <xml name="input_conditional_pssm">
         <conditional name="db_opts">
             <param name="db_opts_selector" type="select" label="Protein domain database (PSSM)">
-              <option value="db" selected="True">Locally installed BLAST protein domain database</option>
+              <option value="db" selected="true">Locally installed BLAST protein domain database</option>
               <option value="histdb">BLAST protein domain database from your history</option>
             </param>
             <when value="db">
@@ -241,7 +241,7 @@
     <xml name="input_conditional_choose_db_type">
         <conditional name="db_opts">
             <param name="db_type" type="select" label="Type of BLAST database">
-              <option value="nucl" selected="True">Nucleotide</option>
+              <option value="nucl" selected="true">Nucleotide</option>
               <option value="prot">Protein</option>
             </param>
             <when value="nucl">
@@ -291,7 +291,7 @@
     <xml name="advanced_options">
         <conditional name="adv_opts">
             <param name="adv_opts_selector" type="select" label="Advanced Options">
-              <option value="basic" selected="True">Hide Advanced Options</option>
+              <option value="basic" selected="true">Hide Advanced Options</option>
               <option value="advanced">Show Advanced Options</option>
             </param>
             <when value="basic" />
@@ -304,8 +304,8 @@
         <conditional name="adv_optional_id_files_opts">
             <param name="adv_optional_id_files_opts_selector" type="select"
                    label="Restrict search of database to a given set of ID's"
-		   help="This feature provides a means to exclude ID's from a BLAST database search. The expectation values in the BLAST results are based upon the sequences actually searched, and not on the underlying database. Note this cannot be used when comparing against a FASTA file.">
-                <option value="none" selected="True">No restriction, search the entire database</option>
+                   help="This feature provides a means to exclude ID's from a BLAST database search. The expectation values in the BLAST results are based upon the sequences actually searched, and not on the underlying database. Note this cannot be used when comparing against a FASTA file.">
+                <option value="none" selected="true">No restriction, search the entire database</option>
                 <option value="gilist">GI identifiers</option>
                 <option value="negative_gilist">Negative GI identifiers</option>
                 <option value="seqidlist">Sequence identifiers (SeqId's)</option>
diff -r c5f20ca77de2 -r 771b554bc85d tools/ncbi_blast_plus/ncbi_makeblastdb.xml
--- a/tools/ncbi_blast_plus/ncbi_makeblastdb.xml	Wed Apr 26 06:47:08 2017 -0400
+++ b/tools/ncbi_blast_plus/ncbi_makeblastdb.xml	Thu May 18 07:40:33 2017 -0400
@@ -5,7 +5,7 @@
         <import>ncbi_macros.xml</import>
     </macros>
     <expand macro="preamble" />
-    <command detect_errors="aggressive" strict="True">
+    <command detect_errors="aggressive" strict="true">
 python $__tool_directory__/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.
@@ -59,7 +59,7 @@
         <!-- Note this is a mandatory parameter - default should be most recent FASTA file -->
         <param name="input_file" type="data" multiple="true" optional="false" format="fasta" label="Input FASTA files(s)" help="One or more FASTA files" />
         <param name="title" type="text" value="" label="Title for BLAST database" help="This is the database name shown in BLAST search output" />
-        <param name="parse_seqids" type="boolean" truevalue="-parse_seqids" falsevalue="" checked="False" label="Parse the sequence identifiers" help="This is only advised if your FASTA file follows the NCBI naming conventions using pipe '|' symbols" />
+        <param name="parse_seqids" type="boolean" truevalue="-parse_seqids" falsevalue="" checked="false" label="Parse the sequence identifiers" help="This is only advised if your FASTA file follows the NCBI naming conventions using pipe '|' symbols" />
         <param name="hash_index" type="boolean" truevalue="-hash_index" falsevalue="" checked="true" label="Enable the creation of sequence hash values" help="These hash values can then be used to quickly determine if a given sequence data exists in this BLAST database." />
         <!-- SEQUENCE MASKING OPTIONS -->
         <!-- Note this is an optional parameter - default should be NO files -->
@@ -108,7 +108,7 @@
             <param name="title" value="Just 4 human proteins" />
             <param name="parse_seqids" value="" />
             <param name="hash_index" value="true" />
-            <output name="out_file" compare="contains" file="four_human_proteins.fasta.log.txt" ftype="blastdbp">
+            <output name="outfile" compare="contains" file="four_human_proteins.fasta.log.txt" ftype="blastdbp">
                 <extra_files type="file" value="four_human_proteins.fasta.phr" name="blastdb.phr" />
                 <extra_files type="file" value="four_human_proteins.fasta.pin" name="blastdb.pin" lines_diff="2" />
                 <extra_files type="file" value="four_human_proteins.fasta.psq" name="blastdb.psq" />
@@ -127,7 +127,7 @@
             <param name="hash_index" value="true" />
             <param name="taxselect" value="id" />
             <param name="taxid" value="9606" />
-            <output name="out_file" compare="contains" file="four_human_proteins_taxid.fasta.log.txt" ftype="blastdbp">
+            <output name="outfile" compare="contains" file="four_human_proteins_taxid.fasta.log.txt" ftype="blastdbp">
                 <extra_files type="file" value="four_human_proteins_taxid.fasta.phr" name="blastdb.phr" />
                 <extra_files type="file" value="four_human_proteins_taxid.fasta.pin" name="blastdb.pin" lines_diff="2" />
                 <extra_files type="file" value="four_human_proteins_taxid.fasta.psq" name="blastdb.psq" />
@@ -145,7 +145,7 @@
             <param name="parse_seqids" value="" />
             <param name="hash_index" value="true" />
             <param name="mask_data_file" value="segmasker_four_human.maskinfo-asn1" ftype="maskinfo-asn1" />
-            <output name="out_file" compare="contains" file="four_human_proteins.fasta.log.txt" ftype="blastdbp">
+            <output name="outfile" compare="contains" file="four_human_proteins.fasta.log.txt" ftype="blastdbp">
                 <extra_files type="file" value="four_human_proteins.fasta.phr" name="blastdb.phr" />
                 <extra_files type="file" value="four_human_proteins.fasta.pin" name="blastdb.pin" lines_diff="2" />
                 <extra_files type="file" value="four_human_proteins.fasta.psq" name="blastdb.psq" />
@@ -164,7 +164,7 @@
             <param name="hash_index" value="true" />
             <param name="taxselect" value="id" />
             <param name="taxid" value="9606" />
-            <output name="out_file" compare="contains" file="three_human_mRNA.fasta.log.txt" ftype="blastdbn">
+            <output name="outfile" compare="contains" file="three_human_mRNA.fasta.log.txt" ftype="blastdbn">
                 <extra_files type="file" value="three_human_mRNA.fasta.nhr" name="blastdb.nhr" />
                 <extra_files type="file" value="three_human_mRNA.fasta.nin" name="blastdb.nin" lines_diff="2" />
                 <extra_files type="file" value="three_human_mRNA.fasta.nsq" name="blastdb.nsq" />
diff -r c5f20ca77de2 -r 771b554bc85d tools/ncbi_blast_plus/ncbi_makeprofiledb.xml
--- a/tools/ncbi_blast_plus/ncbi_makeprofiledb.xml	Wed Apr 26 06:47:08 2017 -0400
+++ b/tools/ncbi_blast_plus/ncbi_makeprofiledb.xml	Thu May 18 07:40:33 2017 -0400
@@ -5,7 +5,7 @@
         <import>ncbi_macros.xml</import>
     </macros>
     <expand macro="preamble" />
-    <command detect_errors="aggressive" strict="True">
+    <command detect_errors="aggressive" strict="true">
 ##Unlike makeblastdb, makeprofiledb needs directory to exist already:
 mkdir -p $outfile.files_path &amp;&amp;
 makeprofiledb -out '${os.path.join($outfile.files_path, "blastdb")}'
@@ -43,8 +43,8 @@
     </configfiles>
     <inputs>
         <param name="input_file" type="data" multiple="true" optional="false" format="pssm-asn1"
-	       label="Input PSSM files(s)"
-	       help="One or NCBI PSSM ASN.1 format scoremat files (often named *.smp)" />
+               label="Input PSSM files(s)"
+               help="One or NCBI PSSM ASN.1 format scoremat files (often named *.smp)" />
         <param name="infile_list" type="data" multiple="true" format="pssm-asn1" />
 
         <param name="title" type="text" value="" label="Title for the profile database" help="This is the database name shown in BLAST search output" />
@@ -61,7 +61,7 @@
 
         <conditional name="contain_pssm_scores">
             <param name="contain_pssm_scores_type" type="select" label="Does your input file contain PSSM scores?">
-              <option value="yes" selected="True">Yes</option>
+              <option value="yes" selected="true">Yes</option>
               <option value="no">No</option>
             </param>
             <when value="yes" />
@@ -89,7 +89,7 @@
             <param name="input_file" value="cd00003.smp,cd00008.smp" ftype="pssm-asn1" />
             <param name="title" value="Just 2 PSSM matrices" />
             <param name="contain_pssm_scores_type" value="yes" />
-            <output name="out_file" file="empty_file.dat" ftype="blastdbd" >
+            <output name="outfile" file="empty_file.dat" ftype="blastdbd" >
                 <extra_files type="file" value="cd00003_and_cd00008.phr" name="blastdb.phr" />
                 <extra_files type="file" value="cd00003_and_cd00008.pin" name="blastdb.pin" lines_diff="2" />
                 <extra_files type="file" value="cd00003_and_cd00008.psq" name="blastdb.psq" />
diff -r c5f20ca77de2 -r 771b554bc85d tools/ncbi_blast_plus/ncbi_segmasker_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_segmasker_wrapper.xml	Wed Apr 26 06:47:08 2017 -0400
+++ b/tools/ncbi_blast_plus/ncbi_segmasker_wrapper.xml	Thu May 18 07:40:33 2017 -0400
@@ -42,9 +42,9 @@
             <change_format>
                 <when input="outformat" value="fasta" format="fasta" />
                 <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>