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comparison reago.xml @ 1:31a354009216 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
author rnateam
date Thu, 02 Feb 2017 19:35:52 -0500
parents 715b263db9f3
children
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0:715b263db9f3 1:31a354009216
1 <tool id="reago" name="Reago" version="0.1.0"> 1 <tool id="reago" name="Reago" version="1.1">
2 <description> to assemble rRNA</description> 2 <description> to assemble rRNA</description>
3 3
4 <requirements> 4 <requirements>
5 <requirement type="package" version="1.1">infernal</requirement>
6 <requirement type="package" version="1.5.7">genometools</requirement>
7 <requirement type="package" version="1.1">reago</requirement> 5 <requirement type="package" version="1.1">reago</requirement>
8 </requirements> 6 </requirements>
9 7
10 <stdio> 8 <stdio>
11 <exit_code range="1:" /> 9 <exit_code range="1:" />
21 --r2_input "$r2_file" 19 --r2_input "$r2_file"
22 --r1_output $r1_output 20 --r1_output $r1_output
23 --r2_output $r2_output 21 --r2_output $r2_output
24 22
25 && 23 &&
26 python \${REAGO_DIR}/filter_input.py 24 filter_input.py
27 $r1_output 25 $r1_output
28 $r2_output 26 $r2_output
29 . 27 .
30 \${REAGO_DIR}/cm/ 28 \$(dirname \$(which reago.py))/cm/
31 $cm_to_use 29 $cm_to_use
32 "\${GALAXY_SLOTS:-4}" 30 "\${GALAXY_SLOTS:-4}"
33 31
34 && 32 &&
35 python \${REAGO_DIR}/reago.py 33 reago.py
36 "filtered.fasta" 34 "filtered.fasta"
37 . 35 .
38 -l $read_length 36 -l $read_length
39 -o $overlap 37 -o $overlap
40 -t $tip_size 38 -t $tip_size