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comparison stringtie_merge.xml @ 14:0f5a352b3f04 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65beed7b9259920d3fdb293a1c7060860bd83594
author iuc
date Tue, 21 Mar 2017 03:07:08 -0400
parents fde005a389b1
children 457d00d0005d
comparison
equal deleted inserted replaced
13:fde005a389b1 14:0f5a352b3f04
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?**