diff pal_finder_wrapper.xml @ 14:3f8bf1a0403b draft

Uploaded version with bad primer ranger detection (WIP).

--- a/pal_finder_wrapper.xml	Thu Mar 15 11:52:19 2018 -0400
+++ b/pal_finder_wrapper.xml	Thu Mar 22 07:21:26 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="microsat_pal_finder" name="pal_finder" version="0.02.04.6">
+<tool id="microsat_pal_finder" name="pal_finder" version="0.02.04.7">
   <description>Find microsatellite repeat elements from sequencing reads and design PCR primers to amplify them</description>
   <macros>
     <import>pal_finder_macros.xml</import>
@@ -26,6 +26,9 @@
     --454 "$platform.input_fasta"
   #end if
   $output_microsat_summary $output_pal_summary
+  #if $report_bad_primer_ranges
+    --bad_primer_ranges "$output_bad_primer_read_ids"
+  #end if
   #if $keep_config_file
     --output_config_file "$output_config_file"
   #end if
@@ -156,6 +159,7 @@
 	       help="Temperature should be in degrees Celsius" />
       </when>
     </conditional>
+    <param name="report_bad_primer_ranges" type="boolean" truevalue="True" falsevalue="False" label="Output IDs for input reads which generate bad primer ranges" help="Can be used to screen input Fastqs" />
     <param name="keep_config_file" type="boolean" truevalue="True" falsevalue="False"
 	   label="Output the config file to the history"
 	   help="Can be used to run pal_finder outside of Galaxy" />
@@ -169,6 +173,9 @@
     <data name="output_assembly" format="tabular" label="${tool.name} on ${on_string} for ${primer_prefix}: assembly">
       <filter>platform['assembly'] is True</filter>
     </data>
+    <data name="output_bad_primer_read_ids" format="tabular" label="${tool.name} on ${on_string} for ${primer_prefix}: read IDs generating bad primer ranges">
+      <filter>report_bad_primer_ranges is True</filter>
+    </data>
     <data name="output_config_file" format="txt" label="${tool.name} on ${on_string} for ${primer_prefix}: config file">
       <filter>keep_config_file is True</filter>
     </data>
@@ -247,6 +254,19 @@
       <output name="output_pal_summary" compare="re_match" file="illuminaPE_microsats.out.re_match" />
       <output name="output_filtered_microsats" compare="re_match" file="illuminaPE_filtered_microsats_rankmotifs.out.re_match" />
     </test>
+    <!-- Test with Illumina input generating bad primer ranges
+    -->
+    <test>
+      <param name="platform_type" value="illumina" />
+      <param name="filters" value="" />
+      <param name="assembly" value="false" />
+      <param name="input_fastq_r1" value="illuminaPE_r1.fq" ftype="fastqsanger" />
+      <param name="input_fastq_r2" value="illuminaPE_r2.fq" ftype="fastqsanger" />
+      <param name="output_bad_primer_read_ids" value="true" />
+      <expand macro="output_illumina_microsat_summary" />
+      <output name="output_pal_summary" compare="re_match" file="illuminaPE_microsats.out.re_match" />
+      <output name="output_bad_primer_read_ids" file="illuminaPE_bad_primer_ids.out" />
+    </test>
     <!-- Test with 454 input -->
     <test>
       <param name="platform_type" value="454" />
@@ -280,6 +300,29 @@
 
 -------------
 
+.. class:: warning
+
+**Known problems**
+
+.. class:: infomark
+
+**Bad primer product size ranges**
+
+For some datasets pal_finder may generate 'bad' product size ranges (where the
+lower limit exceeds the upper limit) for one or more reads, for input into
+primer3_core.
+
+If this occurs then the tool will terminate with an error. A list of the reads
+for which the bad ranges were generated can be found in the error message
+which can be accessed via the 'bug' icon from a failed dataset.
+
+The conditions which cause this error are unclear. However we believe it to be
+associated with short or low quality reads. It is recommended that the input
+data are sufficiently trimmed and filtered (using e.g. the Trimmomatic tool)
+before rerunning pal_finder.
+
+-------------
+
 .. class:: infomark
 
 **Credits**