# HG changeset patch # User matthias # Date 1545155441 18000 # Node ID 7aec316566cb9cf9356560433e3c0719be34c73a # Parent 324a729c257f9ef978d227e94d30c1b49c38fdd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73 diff -r 324a729c257f -r 7aec316566cb macros.xml --- a/macros.xml Fri Nov 30 07:31:49 2018 -0500 +++ b/macros.xml Tue Dec 18 12:50:41 2018 -0500 @@ -8,7 +8,7 @@ 2.2 - 1 + 2 @@ -128,6 +128,7 @@ + @@ -139,7 +140,7 @@ - + @@ -147,30 +148,33 @@ appends noting/.1/.2 to the link name for accessing the fastq data sets variables $name and $data_path--> @@ -188,15 +192,6 @@ #end for ]]> - - - - - - - - - - - - + + + - - - - - - - + + + + + + + diff -r 324a729c257f -r 7aec316566cb macros_process.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros_process.xml Tue Dec 18 12:50:41 2018 -0500 @@ -0,0 +1,235 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + ? + #set $name=$clean_ext($input.name) + #end if + + #if $isfq: + #set $ext = "fastq" + #set inputype = "fastq" + #else + #set $ext = "fastq.gz" + #set inputype = "gzfastq" + #end if + + #if $input_type.options_type_selector == "single" + ln -s '$input' 'stacks_inputs/${name}.${ext}' && + #else: + ## procrad needs _R[12]_ in the file name, so we add an add 0 + ln -s '$input.forward' 'stacks_inputs/${name}_R1_0.${ext}' && + ln -s '$input.reverse' 'stacks_inputs/${name}_R2_0.${ext}' && + #end if + #end for + ]]> + + + + + + + + + + + + + + + + + + + + + + + + input_type['options_type_selector'] == "single" + + + + input_type['options_type_selector'] == "paired" + + + + + input_type['options_type_selector'] == "paired" + + + + + + capture is True and input_type['options_type_selector'] == "single" + + + + capture is True and input_type['options_type_selector'] == "paired" + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r 324a729c257f -r 7aec316566cb stacks_kmerfilter.xml --- a/stacks_kmerfilter.xml Fri Nov 30 07:31:49 2018 -0500 +++ b/stacks_kmerfilter.xml Tue Dec 18 12:50:41 2018 -0500 @@ -7,9 +7,7 @@ +#end if - #if $oligo_len_1 - --oligo_len_1 $oligo_len_1 - #end if - #if $oligo_len_2 - --oligo_len_2 $oligo_len_2 - #end if - $data_type.barcode_encoding - $retain_oligo - -y gzfastq ]]> @@ -70,17 +75,10 @@ - - - - - - - @@ -90,32 +88,38 @@
+ + +
- - -
- +
-
- -
+
- data_type['dt_select'] == 'single' + data_type['dt_select'] == 'single' and not options_kmer_char['k_dist'] - data_type['dt_select'] == 'pair' + data_type['dt_select'] == 'pair' and not options_kmer_char['k_dist'] data_type['dt_select'] == 'pair' + + options_kmer_char['write_k_freq'] + + + options_kmer_char['k_dist'] + @@ -123,9 +127,18 @@ - + + + + + +
+ +
+ +