# 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
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+ 2
@@ -128,6 +128,7 @@
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@@ -139,7 +140,7 @@
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@@ -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
]]>
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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 @@
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+ ?
+ #set $name=$clean_ext($input.name)
+ #end if
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+ #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
+ ]]>
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+ input_type['options_type_selector'] == "single"
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+ input_type['options_type_selector'] == "paired"
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+ input_type['options_type_selector'] == "paired"
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+ capture is True and input_type['options_type_selector'] == "single"
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+ capture is True and input_type['options_type_selector'] == "paired"
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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 @@
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@@ -90,32 +88,38 @@
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- 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'
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+ options_kmer_char['write_k_freq']
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+ options_kmer_char['k_dist']
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@@ -123,9 +127,18 @@
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