Repository 'cutadapt'
hg clone https://toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt

Changeset 13:f5fdf41c08b8 (2018-06-12)
Previous changeset 12:78e1cf88d133 (2018-05-24) Next changeset 14:c76ee709ffb9 (2018-08-05)
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
modified:
cutadapt.xml
b
diff -r 78e1cf88d133 -r f5fdf41c08b8 cutadapt.xml
--- a/cutadapt.xml Thu May 24 18:24:08 2018 -0400
+++ b/cutadapt.xml Tue Jun 12 15:38:04 2018 -0400
[
b'@@ -10,138 +10,135 @@\n     <version_command>cutadapt --version</version_command>\n \n     <command detect_errors="exit_code"><![CDATA[\n-\n-        ## Link in the input and output files, so Cutadapt can tell their type\n+## Link in the input and output files, so Cutadapt can tell their type\n \n-        #import re\n-        #set format = "fastq"\n-        #set read1 = "input_f"\n-        #set read2 = "input_r"\n-        #set paired = False\n-        #set library_type = str($library.type)\n-        #if $library_type == \'paired\':\n-        #set paired = True\n-        #set read1 = re.sub(\'[^\\w\\-\\s]\', \'_\', str($library.input_1.element_identifier))\n-        #set read2 = re.sub(\'[^\\w\\-\\s]\', \'_\', str($library.input_2.element_identifier))\n-        #set input_1 = $library.input_1\n-        #set input_2 = $library.input_2\n-        #else if $library_type == \'paired_collection\'\n-        #set paired = True\n-        #set input_1 = $library.input_1.forward\n-        #set input_2 = $library.input_1.reverse\n-        #set read1 = re.sub(\'[^\\w\\-\\s]\', \'_\', str($library.input_1.name))\n-        #else\n-        #set input_1 = $library.input_1\n-        #set read1 = re.sub(\'[^\\w\\-\\s]\', \'_\', str($library.input_1.element_identifier))\n-        #end if\n+#import re\n+#set read1 = "input_f"\n+#set read2 = "input_r"\n+#set paired = False\n+#set library_type = str($library.type)\n+#if $library_type == \'paired\':\n+#set paired = True\n+#set read1 = re.sub(\'[^\\w\\-\\s]\', \'_\', str($library.input_1.element_identifier))\n+#set read2 = re.sub(\'[^\\w\\-\\s]\', \'_\', str($library.input_2.element_identifier))\n+#set input_1 = $library.input_1\n+#set input_2 = $library.input_2\n+#else if $library_type == \'paired_collection\'\n+#set paired = True\n+#set input_1 = $library.input_1.forward\n+#set input_2 = $library.input_1.reverse\n+#set read1 = re.sub(\'[^\\w\\-\\s]\', \'_\', str($library.input_1.name))\n+#else\n+#set input_1 = $library.input_1\n+#set read1 = re.sub(\'[^\\w\\-\\s]\', \'_\', str($library.input_1.element_identifier))\n+#end if\n \n-        #if $input_1.is_of_type("fastq.gz", "fastqsanger.gz"):\n-            #set read1 = $read1 + ".fq.gz"\n-            #set out1 = "out1.gz"\n-        #else if $input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):\n-            #set read1 = $read1 + ".fq.bz2"\n-            #set out1 = "out1.bz2"\n-        #else if $input_1.is_of_type(\'fasta\'):\n-            #set format = "fasta"\n-            #set read1 = $read1 + ".fa"\n-            #set out1 = "out1.fa"\n-        #else:\n-            #set read1 = $read1 + ".fq"\n-            #set out1 = "out1.fq"\n-        #end if\n-        ln -f -s \'${input_1}\' \'$read1\' &&\n+#if $input_1.is_of_type("fastq.gz", "fastqsanger.gz"):\n+    #set read1 = $read1 + ".fq.gz"\n+    #set out1 = "out1.gz"\n+#else if $input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):\n+    #set read1 = $read1 + ".fq.bz2"\n+    #set out1 = "out1.bz2"\n+#else if $input_1.is_of_type(\'fasta\'):\n+    #set read1 = $read1 + ".fa"\n+    #set out1 = "out1.fa"\n+#else:\n+    #set read1 = $read1 + ".fq"\n+    #set out1 = "out1.fq"\n+#end if\n+ln -f -s \'${input_1}\' \'$read1\' &&\n \n-        #if $paired:\n-            #if $input_2.is_of_type("fastq.gz", "fastqsanger.gz"):\n-                #set read2 = $read2 + ".fq.gz"\n-                #set out2 = "out2.gz"\n-            #else if $input_2.is_of_type("fastq.bz2", "fastqsanger.bz2"):\n-                #set read2 = $read2 + ".fq.bz2"\n-                #set out2 = "out2.bz2"\n-            #else if $input_2.is_of_type(\'fasta\'):\n-                #set format = "fasta"\n-                #set read2 = $read2 + ".fa"\n-                #set out2 = "out2.fa"\n-            #else:\n-                #set read2 = $read2 + ".fq"\n-                #set out2 = "out2.fq"\n-            #end if\n-            ln -f -s \'${input_2}\' \'$read2\' &&\n-        #end if\n+#if $paired:\n+    #if $input_2.is_of_type("fastq.gz", "fastqsanger.gz"):\n+        #set read2 = $read2 + ".fq.gz"\n+        #set out2 = "out2.gz"\n+    #else if $input_2.is_of_type("fastq.bz2", "fastqsanger.bz2"):\n+        #set read2 = $read2 + ".fq.bz2'..b' run in multicore mode with these options\n+#if not any(($output_options.info_file, $output_options.rest_file, $output_options.wildcard_file, $output_options.too_short_file, $output_options.too_long_file, $output_options.untrimmed_file))\n+     -j \\${GALAXY_SLOTS:-1}\n+#end if\n \n-       #if str( $library.type ) == "single":\n-            @read1_options@\n-            --output=\'$out1\'\n-        #else:\n-            @read1_options@\n-            @read2_options@\n-            --output=\'$out1\'\n-            --paired-output=\'$out2\'\n-        #end if\n+#if str( $library.type ) == "single":\n+    @read1_options@\n+    --output=\'$out1\'\n+#else:\n+    @read1_options@\n+    @read2_options@\n+    --output=\'$out1\'\n+    --paired-output=\'$out2\'\n+#end if\n \n-        --error-rate=$adapter_options.error_rate\n-        --times=$adapter_options.count\n-        --overlap=$adapter_options.overlap\n-        $adapter_options.no_indels\n-        $adapter_options.match_read_wildcards\n+--error-rate=$adapter_options.error_rate\n+--times=$adapter_options.count\n+--overlap=$adapter_options.overlap\n+$adapter_options.no_indels\n+$adapter_options.match_read_wildcards\n \n \n-        $filter_options.discard\n-        $filter_options.discard_untrimmed\n-        $filter_options.no_trim\n-        $filter_options.mask_adapter\n-        #if str($filter_options.min) != \'0\':\n-            --minimum-length=$filter_options.min\n-        #end if\n-        #if str($filter_options.max) != \'0\':\n-            --maximum-length=$filter_options.max\n-        #end if\n-        #if $filter_options.max_n:\n-            --max-n=$filter_options.max_n\n-        #end if\n-        #if str( $library.type ) != "single":\n-            #if $filter_options.pair_filter:\n-                --pair-filter=$filter_options.pair_filter\n-            #end if\n-        #end if\n+$filter_options.discard\n+$filter_options.discard_untrimmed\n+$filter_options.no_trim\n+$filter_options.mask_adapter\n+#if str($filter_options.min) != \'0\':\n+    --minimum-length=$filter_options.min\n+#end if\n+#if str($filter_options.max) != \'0\':\n+    --maximum-length=$filter_options.max\n+#end if\n+#if $filter_options.max_n:\n+    --max-n=$filter_options.max_n\n+#end if\n+#if str( $library.type ) != "single":\n+    #if $filter_options.pair_filter:\n+        --pair-filter=$filter_options.pair_filter\n+    #end if\n+#end if\n \n \n-        #if str($read_mod_options.quality_cutoff) != \'0\':\n-           --quality-cutoff=$read_mod_options.quality_cutoff\n-        #end if\n-        #if str($read_mod_options.nextseq_trim) != \'0\':\n-            --nextseq-trim=$read_mod_options.nextseq_trim\n-        #end if\n-        $read_mod_options.trim_n\n-        #if $read_mod_options.prefix != \'\':\n-            --prefix="$read_mod_options.prefix"\n-        #end if\n-        #if $read_mod_options.suffix != \'\':\n-            --suffix="$read_mod_options.suffix"\n-        #end if\n-        #if str($read_mod_options.length) != \'0\':\n-            --length=$$read_mod_options.length\n-        #end if\n-        #if $read_mod_options.length_tag != \'\':\n-            --length-tag="$read_mod_options.length_tag"\n-        #end if\n+#if str($read_mod_options.quality_cutoff) != \'0\':\n+   --quality-cutoff=$read_mod_options.quality_cutoff\n+#end if\n+#if str($read_mod_options.nextseq_trim) != \'0\':\n+    --nextseq-trim=$read_mod_options.nextseq_trim\n+#end if\n+$read_mod_options.trim_n\n+#if $read_mod_options.prefix != \'\':\n+    --prefix="$read_mod_options.prefix"\n+#end if\n+#if $read_mod_options.suffix != \'\':\n+    --suffix="$read_mod_options.suffix"\n+#end if\n+#if str($read_mod_options.length) != \'0\':\n+    --length=$$read_mod_options.length\n+#end if\n+#if $read_mod_options.length_tag != \'\':\n+    --length-tag="$read_mod_options.length_tag"\n+#end if\n \n-        \'${read1}\'\n-        #if $paired:\n-            \'${read2}\'\n-        #end if\n+\'${read1}\'\n+#if $paired:\n+    \'${read2}\'\n+#end if\n \n-        #if $output_options.report:\n-            > report.txt\n-        #end if\n+#if $output_options.report:\n+    > report.txt\n+#end if\n     ]]></command>\n     <inputs>\n \n'