Mercurial > repos > peterjc > mira4_assembler

comparison tools/mira4_0/mira4_de_novo.xml @ 36:46d73b942b43 draft

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planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 9526de68e38a82bb84b2d9267a8c290c6adcaa65
author peterjc
date Fri, 15 Sep 2017 10:09:14 -0400
parents 259891fce7fd
children eeeb21870a73
comparison
equal deleted inserted replaced
35:259891fce7fd 36:46d73b942b43
36 ## 36 ##
37 ## -DI:trt is short for -DIRECTORY:tmp_redirected_to and should 37 ## -DI:trt is short for -DIRECTORY:tmp_redirected_to and should
38 ## point to a local hard drive (not something like NFS on network). 38 ## point to a local hard drive (not something like NFS on network).
39 ## We replace /tmp with an environment variable via mira4.py 39 ## We replace /tmp with an environment variable via mira4.py
40 ## 40 ##
41 ## -OUT:orc=no is short for -OUTPUT:output_result_caf=no 41 ## -OUT:orc=no is short for -OUTPUT:output_result_caf=no
42 ## which turns off an output file we don't want anyway. 42 ## which turns off an output file we don't want anyway.
43 43
44 #for $rg in $read_group 44 #for $rg in $read_group
45 45
46 ##This bar goes into the manifest as a comment line 46 ##This bar goes into the manifest as a comment line
140 <filter>bam_wanted is True</filter> 140 <filter>bam_wanted is True</filter>
141 </data> 141 </data>
142 <data name="out_maf" format="mira" label="MIRA de novo assembly"> 142 <data name="out_maf" format="mira" label="MIRA de novo assembly">
143 <filter>maf_wanted is True</filter> 143 <filter>maf_wanted is True</filter>
144 </data> 144 </data>
145 <!-- TODO? 145 <!-- TODO?
146 <data name="out_contigstats" format="tabular" label="MIRA contig stats" /> 146 <data name="out_contigstats" format="tabular" label="MIRA contig stats" />
147 --> 147 -->
148 <data name="out_log" format="txt" label="MIRA de novo log" /> 148 <data name="out_log" format="txt" label="MIRA de novo log" />
149 </outputs> 149 </outputs>
150 <tests> 150 <tests>
151 <!-- Tiger mitochondria, selected paired end Illumina reads from SRR639755 151 <!-- Tiger mitochondria, selected paired end Illumina reads from SRR639755