# HG changeset patch
# User jackcurragh
# Date 1657632176 0
# Node ID 7b142d90bb0638908680cd6ee51d9c9b991b40a1
# Parent  7065bba6e7cdca78f4331439c528d6299a39b2d7
Uploaded

diff -r 7065bba6e7cd -r 7b142d90bb06 bowtie_rRNA_removal_wrapper/bowtie_rRNA_tRNA_removal_wrapper.py
--- a/bowtie_rRNA_removal_wrapper/bowtie_rRNA_tRNA_removal_wrapper.py	Fri May 27 10:28:39 2022 +0000
+++ b/bowtie_rRNA_removal_wrapper/bowtie_rRNA_tRNA_removal_wrapper.py	Tue Jul 12 13:22:56 2022 +0000
@@ -392,7 +392,19 @@
                 keepends = '--col-keepends'
             else:
                 keepends = ''
-            aligning_cmds = '-q %s %s -p %s -S %s %s %s %s %s %s %s %s %s %s %s %s ' \
+            if options.output_unmapped_reads_l or options.output_unmapped_reads_r or options.output_unmapped_reads:
+                aligning_cmds = '-q %s %s -p %s %s %s %s %s %s %s %s %s %s %s %s %s ' \
+                            '%s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s ' % \
+                            ( maxInsert, mateOrient, options.threads, suppressHeader,
+                              colorspace, skip, alignLimit, trimH, trimL, maxMismatches,
+                              mismatchSeed, mismatchQual, seedLen, rounding, minInsert,
+                              maxAlignAttempt, forwardAlign, reverseAlign, maxBacktracks,
+                              tryHard, valAlign, allValAligns, suppressAlign, best,
+                              strata, offrate, seed, snpphred, snpfrac, keepends,
+                              output_unmapped_reads, output_suppressed_reads,
+                              quality_score_encoding )
+            else:
+                aligning_cmds = '-q %s %s -p %s -S %s %s %s %s %s %s %s %s %s %s %s %s ' \
                             '%s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s ' % \
                             ( maxInsert, mateOrient, options.threads, suppressHeader,
                               colorspace, skip, alignLimit, trimH, trimL, maxMismatches,
diff -r 7065bba6e7cd -r 7b142d90bb06 bowtie_rRNA_removal_wrapper/bowtie_rRNA_tRNA_removal_wrapper.xml
--- a/bowtie_rRNA_removal_wrapper/bowtie_rRNA_tRNA_removal_wrapper.xml	Fri May 27 10:28:39 2022 +0000
+++ b/bowtie_rRNA_removal_wrapper/bowtie_rRNA_tRNA_removal_wrapper.xml	Tue Jul 12 13:22:56 2022 +0000
@@ -222,7 +222,7 @@
         <option value="paired">Paired-end</option>
       </param>
       <when value="single">
-        <param name="sInput1" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="FASTQ file" help="Must have ASCII encoded quality scores"/>
+        <param name="sInput1" type="data" format="fastqsanger,fastqillumina,fastqsolexa,fastq" label="FASTQ file" help="Must have ASCII encoded quality scores"/>
         <conditional name="sParams">
           <param name="sSettingsType" type="select" label="Bowtie settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full parameter list">
             <option value="preSet">Commonly used</option>