From 477fa234a200919cbef851462b59e2ed016aad26 Mon Sep 17 00:00:00 2001
From: curtis <curtis@groov.dev>
Date: Wed, 22 Mar 2023 20:43:13 -0500
Subject: [PATCH] Comb through and use CDATA

CDATA for proper > usage

[#1]
---
 blast/nuc_relate.xml                                | 4 ++--
 blast/prot_relate.xml                               | 4 ++--
 comparative/mist3.xml                               | 4 ++--
 cpt_convert_glimmer/cpt_convert_glimmer_to_gff3.xml | 4 ++--
 cpt_convert_mga/cpt_convert_mga_to_gff3.xml         | 5 ++---
 cpt_fasta_charges/fasta_charges.xml                 | 4 ++--
 cpt_fasta_remove_id/fasta_remove_id.xml             | 4 ++--
 cpt_get_orfs/get_orfs_or_cdss.xml                   | 4 ++--
 cpt_mist3/mist3.xml                                 | 6 +++---
 cpt_related_genome_nuc/nuc_relate.xml               | 4 ++--
 cpt_related_genome_prot/prot_relate.xml             | 4 ++--
 fasta/fasta_remove_id.xml                           | 4 ++--
 fasta/get_orfs_or_cdss.xml                          | 4 ++--
 util/cpt_convert_glimmer_to_gff3.xml                | 4 ++--
 util/cpt_convert_mga_to_gff3.xml                    | 4 ++--
 15 files changed, 31 insertions(+), 32 deletions(-)

diff --git a/blast/nuc_relate.xml b/blast/nuc_relate.xml
index da95b28..93f0073 100755
--- a/blast/nuc_relate.xml
+++ b/blast/nuc_relate.xml
@@ -5,14 +5,14 @@
         <import>cpt-macros.xml</import>
     </macros>
     <expand macro="requirements"/>
-    <command detect_errors="aggressive">
+    <command detect_errors="aggressive"><![CDATA[
 '$__tool_directory__/relatedness.py'
 @BLAST_TSV@
 '$__tool_directory__/TaxID_List.txt'
 '$access'
 '$filter'
 --hits '$hits'
-&gt; '$accession_list'
+> '$accession_list']]>
 </command>
     <inputs>
         <expand macro="blast_tsv"/>
diff --git a/blast/prot_relate.xml b/blast/prot_relate.xml
index 3ab93ea..bf33339 100755
--- a/blast/prot_relate.xml
+++ b/blast/prot_relate.xml
@@ -5,14 +5,14 @@
         <import>cpt-macros.xml</import>
     </macros>
     <expand macro="requirements"/>
-    <command detect_errors="aggressive">
+    <command detect_errors="aggressive"><![CDATA[
 '$__tool_directory__/relatedness_prot.py'
 @BLAST_TSV@
 '$__tool_directory__/TaxID_List.txt'
 --hits '$hits'
 '$filter'
 --protein
-&gt; '$accession_list'
+> '$accession_list']]>
 </command>
     <inputs>
         <expand macro="blast_tsv"/>
diff --git a/comparative/mist3.xml b/comparative/mist3.xml
index c35ce5d..11c11c7 100755
--- a/comparative/mist3.xml
+++ b/comparative/mist3.xml
@@ -10,7 +10,7 @@
         <requirement type="package" version="7.0.8_68">imagemagick</requirement>
         <requirement type="package" version="9.18">ghostscript</requirement>
     </expand>
-    <command detect_errors="aggressive">
+    <command detect_errors="aggressive"><![CDATA[
 '$__tool_directory__/mist3.py'
 #set repeat_var_1 = '" "'.join([ str($var) for $var in $fasta_files ])
 --window "${window}"
@@ -20,7 +20,7 @@
 --plot_type '$plot_type'
 
 "$repeat_var_1"
-&gt; '$output'
+> '$output' ]]>
 </command>
     <inputs>
         <param help="Sequences to plot" label="file" name="fasta_files" type="data" format="fasta" multiple="True"/>
diff --git a/cpt_convert_glimmer/cpt_convert_glimmer_to_gff3.xml b/cpt_convert_glimmer/cpt_convert_glimmer_to_gff3.xml
index c41922a..707468c 100755
--- a/cpt_convert_glimmer/cpt_convert_glimmer_to_gff3.xml
+++ b/cpt_convert_glimmer/cpt_convert_glimmer_to_gff3.xml
@@ -5,13 +5,13 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements"/>
-    <command detect_errors="aggressive">
+    <command detect_errors="aggressive"><![CDATA[
 @GENOME_SELECTOR_PRE@
 
 'python $__tool_directory__/cpt_convert_glimmer_to_gff3.py'
 '$glimmer'
 @GENOME_SELECTOR@
-&gt; '$data'
+> '$data' ]]>
 </command>
     <inputs>
         <param label="Glimmer Output" name="glimmer" type="data" format="tabular,txt"/>
diff --git a/cpt_convert_mga/cpt_convert_mga_to_gff3.xml b/cpt_convert_mga/cpt_convert_mga_to_gff3.xml
index b195e95..023a2f8 100755
--- a/cpt_convert_mga/cpt_convert_mga_to_gff3.xml
+++ b/cpt_convert_mga/cpt_convert_mga_to_gff3.xml
@@ -5,14 +5,13 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements"/>
-    <command detect_errors="aggressive">
+    <command detect_errors="aggressive"><![CDATA[
 @GENOME_SELECTOR_PRE@
 
 python '$__tool_directory__/cpt_convert_mga_to_gff3.py'
 '$mga'
 @GENOME_SELECTOR@
-&gt; '$data'
-
+> '$data' ]]>
 </command>
     <inputs>
         <param label="MGA Output" name="mga" type="data" format="txt"/>
diff --git a/cpt_fasta_charges/fasta_charges.xml b/cpt_fasta_charges/fasta_charges.xml
index dd8e53e..402d2bc 100755
--- a/cpt_fasta_charges/fasta_charges.xml
+++ b/cpt_fasta_charges/fasta_charges.xml
@@ -5,7 +5,7 @@
         <import>cpt-macros.xml</import>
     </macros>
     <expand macro="requirements"/>
-    <command detect_errors="aggressive">
+    <command detect_errors="aggressive"><![CDATA[
 '$__tool_directory__/fasta_charges.py'
 '$svg'
 @SEQUENCE@
@@ -39,7 +39,7 @@
 	#end for
 #end if
 
-&gt; $html
+> $html ]]>
 </command>
     <inputs>
         <expand macro="input/fasta/protein"/>
diff --git a/cpt_fasta_remove_id/fasta_remove_id.xml b/cpt_fasta_remove_id/fasta_remove_id.xml
index 9160b0f..cbee5e2 100755
--- a/cpt_fasta_remove_id/fasta_remove_id.xml
+++ b/cpt_fasta_remove_id/fasta_remove_id.xml
@@ -5,10 +5,10 @@
         <import>cpt-macros.xml</import>
     </macros>
     <expand macro="requirements"/>
-    <command detect_errors="aggressive">
+    <command detect_errors="aggressive"><![CDATA[
 '$__tool_directory__/fasta_remove_id.py'
 @SEQUENCE@
-&gt; '$out'
+> '$out' ]]>
 </command>
     <inputs>
         <expand macro="input/fasta"/>
diff --git a/cpt_get_orfs/get_orfs_or_cdss.xml b/cpt_get_orfs/get_orfs_or_cdss.xml
index 4761d72..f59bc06 100755
--- a/cpt_get_orfs/get_orfs_or_cdss.xml
+++ b/cpt_get_orfs/get_orfs_or_cdss.xml
@@ -7,8 +7,8 @@
     <expand macro="requirements">
         <requirement type="package" version="2022.1.18">regex</requirement>
     </expand>
-    <command interpreter="python" detect_errors="aggressive">
-get_orfs_or_cdss.py '$input_file' -f '$input_file.ext' --table '$table' -t '$ftype' -e "closed" -m "all" --min_len '$min_len' --strand '$strand' --on '$out_nuc_file' --op '$out_prot_file' --ob '$out_bed_file' --og '$out_gff3_file'
+    <command interpreter="python" detect_errors="aggressive"><![CDATA[
+get_orfs_or_cdss.py '$input_file' -f '$input_file.ext' --table '$table' -t '$ftype' -e "closed" -m "all" --min_len '$min_len' --strand '$strand' --on '$out_nuc_file' --op '$out_prot_file' --ob '$out_bed_file' --og '$out_gff3_file' ]]>
 	</command>
     <inputs>
         <param name="input_file" type="data" format="fasta,fastq,sff" label="Sequence file (nucleotides)" help="FASTA, FASTQ, or SFF format."/>
diff --git a/cpt_mist3/mist3.xml b/cpt_mist3/mist3.xml
index f3283d7..c31f17c 100755
--- a/cpt_mist3/mist3.xml
+++ b/cpt_mist3/mist3.xml
@@ -11,8 +11,8 @@
         <requirement type="package" version="7.0.8_68">imagemagick</requirement>
         <requirement type="package" version="9.18">ghostscript</requirement>
     </requirements>
-    <command detect_errors="aggressive">'
-$__tool_directory__/mist3.py'
+    <command detect_errors="aggressive"><![CDATA[
+'$__tool_directory__/mist3.py'
 #set repeat_var_1 = '" "'.join([ str('$var') for '$var' in '$fasta_files' ])
 --window "${window}"
 --zoom "${zoom}"
@@ -21,7 +21,7 @@ $__tool_directory__/mist3.py'
 --plot_type '$plot_type'
 
 "$repeat_var_1"
-&gt; '$output'
+> '$output' ]]>
 </command>
     <inputs>
         <param help="Sequences to plot" label="file" name="fasta_files" type="data" format="fasta" multiple="True"/>
diff --git a/cpt_related_genome_nuc/nuc_relate.xml b/cpt_related_genome_nuc/nuc_relate.xml
index bac6b65..cb252ae 100755
--- a/cpt_related_genome_nuc/nuc_relate.xml
+++ b/cpt_related_genome_nuc/nuc_relate.xml
@@ -5,7 +5,7 @@
         <import>cpt-macros.xml</import>
     </macros>
     <expand macro="requirements"/>
-    <command detect_errors="aggressive">
+    <command detect_errors="aggressive"><![CDATA[
 '$__tool_directory__/relatedness.py'
 '${blastIn.blast}'
 '$__tool_directory__/TaxID_List.txt'
@@ -15,7 +15,7 @@
 #if $blastIn.blastType == "XML":
 --xmlMode
 #end if
-&gt; '$accession_list'
+> '$accession_list' ]]>
 </command>
     <inputs>
         <conditional name="blastIn">
diff --git a/cpt_related_genome_prot/prot_relate.xml b/cpt_related_genome_prot/prot_relate.xml
index 41cfd4c..2314914 100755
--- a/cpt_related_genome_prot/prot_relate.xml
+++ b/cpt_related_genome_prot/prot_relate.xml
@@ -5,7 +5,7 @@
         <import>cpt-macros.xml</import>
     </macros>
     <expand macro="requirements"/>
-    <command detect_errors="aggressive">
+    <command detect_errors="aggressive"><![CDATA[
 '$__tool_directory__/relatedness_prot.py'
 '${blastIn.blast}'
 '$__tool_directory__/TaxID_List.txt'
@@ -16,7 +16,7 @@
 --xmlMode
 #end if
 --taxFilter "$taxFilter" 
-&gt; '$accession_list'
+> '$accession_list' ]]>
 </command>
     <inputs>
         <conditional name="blastIn">
diff --git a/fasta/fasta_remove_id.xml b/fasta/fasta_remove_id.xml
index 7c58c79..209ac4c 100755
--- a/fasta/fasta_remove_id.xml
+++ b/fasta/fasta_remove_id.xml
@@ -5,10 +5,10 @@
         <import>cpt-macros.xml</import>
     </macros>
     <expand macro="requirements"/>
-    <command detect_errors="aggressive">
+    <command detect_errors="aggressive"><![CDATA[
 '$__tool_directory__/fasta_remove_id.py'
 @SEQUENCE@
-&gt; '$out'
+> '$out' ]]>
 </command>
     <inputs>
         <expand macro="input/fasta"/>
diff --git a/fasta/get_orfs_or_cdss.xml b/fasta/get_orfs_or_cdss.xml
index c652a46..ee31c76 100755
--- a/fasta/get_orfs_or_cdss.xml
+++ b/fasta/get_orfs_or_cdss.xml
@@ -7,8 +7,8 @@
     <expand macro="requirements">
         <requirement type="package" version="2019.06.08">regex</requirement>
     </expand>
-    <command interpreter="python" detect_errors="aggressive">
-get_orfs_or_cdss.py '$input_file' -f '$input_file.ext' --table '$table' -t '$ftype' -e "closed" -m "all" --min_len '$min_len' --strand '$strand' --on '$out_nuc_file' --op '$out_prot_file' --ob '$out_bed_file' --og '$out_gff3_file'
+    <command interpreter="python" detect_errors="aggressive"><![CDATA[
+get_orfs_or_cdss.py '$input_file' -f '$input_file.ext' --table '$table' -t '$ftype' -e "closed" -m "all" --min_len '$min_len' --strand '$strand' --on '$out_nuc_file' --op '$out_prot_file' --ob '$out_bed_file' --og '$out_gff3_file' ]]>
 	</command>
     <inputs>
         <param name="input_file" type="data" format="fasta,fastq,sff" label="Sequence file (nucleotides)" help="FASTA, FASTQ, or SFF format."/>
diff --git a/util/cpt_convert_glimmer_to_gff3.xml b/util/cpt_convert_glimmer_to_gff3.xml
index 49e0201..f964e84 100755
--- a/util/cpt_convert_glimmer_to_gff3.xml
+++ b/util/cpt_convert_glimmer_to_gff3.xml
@@ -5,13 +5,13 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements"/>
-    <command detect_errors="aggressive">
+    <command detect_errors="aggressive"><![CDATA[
 @GENOME_SELECTOR_PRE@
 
 python '$__tool_directory__/cpt_convert_glimmer_to_gff3.py'
 '$glimmer'
 @GENOME_SELECTOR@
-&gt; '$data'
+> '$data' ]]>
 </command>
     <inputs>
         <param label="Glimmer Output" name="glimmer" type="data" format="tabular,txt"/>
diff --git a/util/cpt_convert_mga_to_gff3.xml b/util/cpt_convert_mga_to_gff3.xml
index 6bc69a8..e406672 100755
--- a/util/cpt_convert_mga_to_gff3.xml
+++ b/util/cpt_convert_mga_to_gff3.xml
@@ -5,13 +5,13 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="requirementsPython3"/>
-    <command detect_errors="aggressive">
+    <command detect_errors="aggressive"><![CDATA[
 @GENOME_SELECTOR_PRE@
 
 python '$__tool_directory__/cpt_convert_mga_to_gff3.py'
 '$mga'
 @GENOME_SELECTOR@
-&gt; '$data'
+> '$data' ]]>
 
 </command>
     <inputs>