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comparison micall_lite.xml @ 1:bb549c5eaf34 draft

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"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 5d661c102f12509d19c8869988c3f2f7ce00732b"
author public-health-bioinformatics
date Wed, 08 Jan 2020 17:43:18 -0500
parents 023064145bea
children e5390c4b69e9
comparison
equal deleted inserted replaced
0:023064145bea 1:bb549c5eaf34
1 <tool id="micall_lite" name="micall_lite" version="@TOOL_VERSION@+galaxy0"> 1 <tool id="micall_lite" name="micall_lite" version="@TOOL_VERSION@+galaxy1">
2 <description></description> 2 <description></description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
10 <command detect_errors="exit_code"> 10 <command detect_errors="exit_code">
11 <![CDATA[ 11 <![CDATA[
12 #if str( $fastq_input.fastq_input_selector ) == "paired": 12 #if str( $fastq_input.fastq_input_selector ) == "paired":
13 #if $fastq_input.reads1.is_of_type("fastq.gz", "fastqsanger.gz"): 13 #if $fastq_input.reads1.is_of_type("fastq.gz", "fastqsanger.gz"):
14 #set unzipped = False 14 #set unzipped = False
15 #set reads1 = $fastq_input.reads1.element_identifier + '_R1.fastq.gz' 15 #set reads1 = $fastq_input.reads1.name + '_R1.fastq.gz'
16 #else if $fastq_input.reads1.is_of_type("fastq", "fastqsanger"): 16 #else if $fastq_input.reads1.is_of_type("fastq", "fastqsanger"):
17 #set unzipped = True 17 #set unzipped = True
18 #set reads1 = $fastq_input.reads1.element_identifier + '_R1.fastq' 18 #set reads1 = $fastq_input.reads1.name + '_R1.fastq'
19 #end if 19 #end if
20 ln -s '$fastq_input.reads1' '$reads1' && 20 ln -s '$fastq_input.reads1' '$reads1' &&
21 #if $fastq_input.reads2.is_of_type("fastq.gz", "fastqsanger.gz"): 21 #if $fastq_input.reads2.is_of_type("fastq.gz", "fastqsanger.gz"):
22 #set unzipped = False 22 #set unzipped = False
23 #set reads2 = $fastq_input.reads2.element_identifier + '_R2.fastq.gz' 23 #set reads2 = $fastq_input.reads2.name + '_R2.fastq.gz'
24 #else if $fastq_input.reads2.is_of_type("fastq", "fastqsanger"): 24 #else if $fastq_input.reads2.is_of_type("fastq", "fastqsanger"):
25 #set unzipped = True 25 #set unzipped = True
26 #set reads2 = $fastq_input.reads2.element_identifier + '_R2.fastq' 26 #set reads2 = $fastq_input.reads2.name + '_R2.fastq'
27 #end if 27 #end if
28 ln -s '$fastq_input.reads2' '$reads2' && 28 ln -s '$fastq_input.reads2' '$reads2' &&
29 #else if str( $fastq_input.fastq_input_selector ) == "paired_collection": 29 #else if str( $fastq_input.fastq_input_selector ) == "paired_collection":
30 #if $fastq_input.pair.forward.is_of_type("fastq.gz", "fastqsanger.gz"): 30 #if $fastq_input.pair.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
31 #set unzipped = False 31 #set unzipped = False
32 #set reads1 = $fastq_input.pair.element_identifier + '_R1.fastq.gz' 32 #set reads1 = $fastq_input.pair.name + '_R1.fastq.gz'
33 #else if $fastq_input.pair.forward.is_of_type("fastq", "fastqsanger"): 33 #else if $fastq_input.pair.forward.is_of_type("fastq", "fastqsanger"):
34 #set unzipped = True 34 #set unzipped = True
35 #set reads1 = $fastq_input.pair.element_identifier + '_R1.fastq' 35 #set reads1 = $fastq_input.pair.name + '_R1.fastq'
36 #end if 36 #end if
37 ln -s '$fastq_input.pair.forward' '$reads1' && 37 ln -s '$fastq_input.pair.forward' '$reads1' &&
38 #if $fastq_input.pair.reverse.is_of_type("fastq.gz", "fastqsanger.gz"): 38 #if $fastq_input.pair.reverse.is_of_type("fastq.gz", "fastqsanger.gz"):
39 #set unzipped = False 39 #set unzipped = False
40 #set reads2 = $fastq_input.pair.element_identifier + '_R2.fastq.gz' 40 #set reads2 = $fastq_input.pair.name + '_R2.fastq.gz'
41 #else if $fastq_input.pair.reverse.is_of_type("fastq", "fastqsanger"): 41 #else if $fastq_input.pair.reverse.is_of_type("fastq", "fastqsanger"):
42 #set unzipped = True 42 #set unzipped = True
43 #set reads2 = $fastq_input.pair.element_identifier + '_R2.fastq' 43 #set reads2 = $fastq_input.pair.name + '_R2.fastq'
44 #end if 44 #end if
45 ln -s '$fastq_input.pair.reverse' '$reads2' && 45 ln -s '$fastq_input.pair.reverse' '$reads2' &&
46 #end if 46 #end if
47 47
48 mkdir 'outdir' && 48 mkdir 'outdir' &&