Mercurial > repos > iuc > nugen_nudup
comparison nugen_nudup.xml @ 2:57a00c4e43ec draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup commit c3b2bf5ee64db2e334711d6f012190f9f7b4ea28
author | iuc |
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date | Fri, 03 Mar 2017 19:35:28 -0500 |
parents | 24693e595caf |
children | 2bad02c1cb0d |
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1:24693e595caf | 2:57a00c4e43ec |
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1 <tool id="nugen_nudup" name="NuDUP" version="2.3.1" profile="17.01"> | 1 <tool id="nugen_nudup" name="NuDUP" version="2.3.2" profile="17.01"> |
2 <description> | 2 <description> |
3 mark/remove PCR duplicates based on molecular tags | 3 mark/remove PCR duplicates based on molecular tags |
4 </description> | 4 </description> |
5 <requirements> | 5 <requirements> |
6 <requirement type="package" version="2.3.1">nudup</requirement> | 6 <requirement type="package" version="2.3.2">nudup</requirement> |
7 </requirements> | 7 </requirements> |
8 <stdio> | 8 <stdio> |
9 <exit_code range="1:" /> | 9 <exit_code range="1:" /> |
10 </stdio> | 10 </stdio> |
11 <version_command>nudup.py --version</version_command> | 11 <version_command>nudup.py --version</version_command> |
18 #else: | 18 #else: |
19 #set umi_file = 'umi.fastq' | 19 #set umi_file = 'umi.fastq' |
20 #end if | 20 #end if |
21 ln -f -s '$umi_fastq' '$umi_file' && | 21 ln -f -s '$umi_fastq' '$umi_file' && |
22 nudup.py | 22 nudup.py |
23 -T \$PWD'/tmp' | 23 -T 'tmp' |
24 $paired_end | 24 $paired_end |
25 -f '$umi_file' | 25 -f '$umi_file' |
26 --start $start | 26 --start $start |
27 --length $length | 27 --length $length |
28 $rmdup_only | 28 $rmdup_only |
144 ]]></help> | 144 ]]></help> |
145 <citations> | 145 <citations> |
146 <citation type="bibtex">@misc{Patel2017, | 146 <citation type="bibtex">@misc{Patel2017, |
147 author = {Patel, Anand}, | 147 author = {Patel, Anand}, |
148 title = {NuDUP}, | 148 title = {NuDUP}, |
149 version = {2.3.2}, | |
149 year = {2017}, | 150 year = {2017}, |
150 publisher = {GitHub}, | 151 publisher = {GitHub}, |
151 journal = {GitHub repository}, | 152 journal = {GitHub repository}, |
152 howpublished = {\url{https://github.com/nugentechnologies/nudup}}, | 153 howpublished = {\url{https://github.com/nugentechnologies/nudup}}, |
153 commit = {7451de86680d24f19638ed6ac88f6504f0817753} | 154 commit = {7a126eb5a4ccc2bacb426c7cf58b351962798093} |
154 } | 155 } |
155 </citation> | 156 </citation> |
156 </citations> | 157 </citations> |
157 </tool> | 158 </tool> |