Mercurial > repos > iuc > stringtie
comparison stringtie_merge.xml @ 9:1f23fc7df25c draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65beed7b9259920d3fdb293a1c7060860bd83594
author | iuc |
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date | Tue, 21 Mar 2017 03:07:22 -0400 |
parents | 3437d5a5041c |
children | c84d44519b2e |
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8:3437d5a5041c | 9:1f23fc7df25c |
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8 <expand macro="version_command" /> | 8 <expand macro="version_command" /> |
9 <command> | 9 <command> |
10 <![CDATA[ | 10 <![CDATA[ |
11 stringtie --merge | 11 stringtie --merge |
12 -p \${GALAXY_SLOTS:-1} | 12 -p \${GALAXY_SLOTS:-1} |
13 #if str($guide_gff) != "": | 13 #if $guide_gff: |
14 -G "$guide_gff" | 14 -G "$guide_gff" |
15 #end if | 15 #end if |
16 -m $min_len | 16 -m $min_len |
17 -c $min_cov | 17 -c $min_cov |
18 -F $min_fpkm | 18 -F $min_fpkm |
23 #set inputs = '" "'.join(str($input_gtf).split(',')) | 23 #set inputs = '" "'.join(str($input_gtf).split(',')) |
24 -o $out_gtf "$inputs" | 24 -o $out_gtf "$inputs" |
25 ]]> | 25 ]]> |
26 </command> | 26 </command> |
27 <inputs> | 27 <inputs> |
28 <param type="data" name="input_gtf" multiple="true" format="gtf,gff3" /> | 28 <param type="data" name="input_gtf" multiple="True" format="gtf,gff3" /> |
29 <param type="data" name="guide_gff" optional="True" format="gtf,gff3" /> | 29 <param type="data" name="guide_gff" optional="True" format="gtf,gff3" /> |
30 <param argument="-m" type="integer" name="min_len" value="50" help="Minimum input transcript length to include in the merge" /> | 30 <param argument="-m" type="integer" name="min_len" value="50" help="Minimum input transcript length to include in the merge" /> |
31 <param argument="-c" type="integer" name="min_cov" value="0" help="Minimum input transcript coverage to include in the merge" /> | 31 <param argument="-c" type="integer" name="min_cov" value="0" help="Minimum input transcript coverage to include in the merge" /> |
32 <param argument="-F" type="float" name="min_fpkm" value="1.0" help="Minimum input transcript FPKM to include in the merge" /> | 32 <param argument="-F" type="float" name="min_fpkm" value="1.0" help="Minimum input transcript FPKM to include in the merge" /> |
33 <param argument="-T" type="float" name="min_tpm" value="1.0" help="Minimum input transcript TPM to include in the merge" /> | 33 <param argument="-T" type="float" name="min_tpm" value="1.0" help="Minimum input transcript TPM to include in the merge" /> |
46 </test> | 46 </test> |
47 <test> | 47 <test> |
48 <param ftype="gtf" name="input_gtf" value="stringtie_merge_in1.gtf,stringtie_merge_in2.gtf" /> | 48 <param ftype="gtf" name="input_gtf" value="stringtie_merge_in1.gtf,stringtie_merge_in2.gtf" /> |
49 <param ftype="gtf" name="guide_gff" value="stringtie_merge_in3.gtf" /> | 49 <param ftype="gtf" name="guide_gff" value="stringtie_merge_in3.gtf" /> |
50 <output file="stringtie_merge_out2.gtf" ftype="gtf" lines_diff="2" name="out_gtf" /> | 50 <output file="stringtie_merge_out2.gtf" ftype="gtf" lines_diff="2" name="out_gtf" /> |
51 </test> | |
52 <test> | |
53 <param ftype="gtf" name="input_gtf" value="stringtie_merge_in1.gtf,stringtie_merge_in2.gtf" /> | |
54 <output ftype="gtf" name="out_gtf"> | |
55 <assert_contents> | |
56 <has_text text="stringtie --merge" /> | |
57 </assert_contents> | |
58 </output> | |
51 </test> | 59 </test> |
52 </tests> | 60 </tests> |
53 <help><![CDATA[ | 61 <help><![CDATA[ |
54 | 62 |
55 **What it does?** | 63 **What it does?** |