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comparison GetHaplotypesFromPhasedVCF/getHaplotypesFromPhasedVCF.xml @ 12:88748d846a20 draft

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planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f
author dereeper
date Tue, 14 Aug 2018 08:21:55 -0400
parents c6640c49fd01
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11:15b23cdde685 12:88748d846a20
6 </requirements> 6 </requirements>
7 <stdio> 7 <stdio>
8 <exit_code range="1:" /> 8 <exit_code range="1:" />
9 </stdio> 9 </stdio>
10 <command interpreter="perl"> 10 <command interpreter="perl">
11 GetHaplotypesFromPhasedVCF.pl $input $output_label &amp;&amp; mv ${output_label}.distinct_haplotypes.txt $output_distinct &amp;&amp; mv ${output_label}.haplo.fas $output_haplo 11 GetHaplotypesFromPhasedVCF.pl $input $output_label &amp;&amp; mv ${output_label}.distinct_haplotypes.txt $output_distinct &amp;&amp; mv ${output_label}.haplo.fas $output_haplo &amp;&amp; mv ${output_label}.distinct_haplotypes.fa $output_distinct_fasta
12 </command> 12 </command>
13 <inputs> 13 <inputs>
14 <param type="data" name="input" format="vcf" label="Phased VCF" /> 14 <param type="data" name="input" format="vcf" label="Phased VCF" />
15 <param type="text" name="output_label" label="Output_label" value='Haplotypes' /> 15 <param type="text" name="output_label" label="Output_label" value='Haplotypes' />
16 </inputs> 16 </inputs>
17 <outputs> 17 <outputs>
18 <data name="output_distinct" format="txt" label="${output_label}.distinct_haplotypes.txt"/> 18 <data name="output_distinct" format="txt" label="${output_label}.distinct_haplotypes.txt"/>
19 <data name="output_haplo" format="fasta" label="${output_label}.haplo.fas"/> 19 <data name="output_haplo" format="fasta" label="${output_label}.haplo.fas"/>
20 <data name="output_distinct_fasta" format="fasta" label="${output_label}.distinct_haplotypes.fa"/>
20 </outputs> 21 </outputs>
21 <tests> 22 <tests>
22 <test> 23 <test>
23 <param name="input" value="getHaplotypesFromPhasedVCF-input.vcf"/> 24 <param name="input" value="getHaplotypesFromPhasedVCF-input.vcf"/>
24 <output name="output_distinct" file="getHaplotypesFromPhasedVCF-result.distinct_haplotypes.txt" compare="sim_size" delta="0"/> 25 <output name="output_distinct" file="getHaplotypesFromPhasedVCF-result.distinct_haplotypes.txt" compare="sim_size" delta="0"/>
25 <output name="output_haplo" file="getHaplotypesFromPhasedVCF-result.haplo.fas" compare="sim_size" delta="0"/> 26 <output name="output_haplo" file="getHaplotypesFromPhasedVCF-result.haplo.fas" compare="sim_size" delta="0"/>
27 <output name="output_distinct_fasta" file="getHaplotypesFromPhasedVCF-result.distinct_haplotypes.fas" compare="sim_size" delta="0"/>
26 </test> 28 </test>
27 </tests> 29 </tests>
28 <help><![CDATA[ 30 <help><![CDATA[
29 31
30 .. class:: infomark 32 .. class:: infomark
70 ------------ 72 ------------
71 Output files 73 Output files
72 ------------ 74 ------------
73 75
74 76
75 Text file 77 Distinct Haplotypes text file
76 File describing haplotypes 78 File describing distincts haplotypes
77 79
78 Fasta file 80 Fasta file
79 Fasta file with haplotypes 81 Fasta file with haplotypes
82
83 Distinct Haplotypes fasta file
84 Fasta file with distincts haplotypes
85
80 86
81 --------------------------------------------------- 87 ---------------------------------------------------
82 88
83 --------------- 89 ---------------
84 Working example 90 Working example
129 >Chr10_AZUCENA_1 135 >Chr10_AZUCENA_1
130 TTTAAGAAATTCCTATATAGGTCTTCTAAGCGTATCTATTAACAT 136 TTTAAGAAATTCCTATATAGGTCTTCTAAGCGTATCTATTAACAT
131 >Chr10_AZUCENA_2 137 >Chr10_AZUCENA_2
132 TAAATCTTGGTGCTGATCTGATATTTAATGCGT 138 TAAATCTTGGTGCTGATCTGATATTTAATGCGT
133 139
140 haplotypes.distinct_haplotypes.fas
141 ----------------------------------
142
143 ::
144
145 >haplo1|2
146 CAATTTATATATACTTGTATATAACCACAACGAGAGAGTTTTACCT
147 TTTATAAAAAATAAATAATGTATTACGGCTAATATAGCAATCTTTT
148 AAAATAAATCTATATTTAAATGACTATGGAATTACTAATCACAATA
149 ACAGGATCTTGTTATTTTTAGCTTGTGTACTTATAATGATCCGATG
150 >haplo2|2
151 GCTACTTAAATATCTAGCATTAATCCACAACGAGAGGCTCTTACCT
152 TTAAAAAAGGGTCATCGCCTATAGGTTAGATAATCGACACATATAA
153 TTATAAGAAATTATATATAATTTTTAATCTAGTTCATTCTTGTGCA
154 TCATTATGTTATATAATAATAAACGTAACAAATATTGATACTACTC
155
156
134 ]]></help> 157 ]]></help>
135 <citations> 158 <citations>
136 <!-- [HELP] As DOI or BibTex entry --> 159 <!-- [HELP] As DOI or BibTex entry -->
137 <citation type="bibtex">@article{Dereeper03062015, 160 <citation type="bibtex">@article{Dereeper03062015,
138 author = {Dereeper, Alexis and Homa, Felix and Andres, Gwendoline and Sempere, Guilhem and Sarah, Gautier and Hueber, Yann and Dufayard, Jean-François and Ruiz, Manuel}, 161 author = {Dereeper, Alexis and Homa, Felix and Andres, Gwendoline and Sempere, Guilhem and Sarah, Gautier and Hueber, Yann and Dufayard, Jean-François and Ruiz, Manuel},