Mercurial > repos > iuc > mothur_make_contigs

comparison make.contigs.xml @ 1:3dab7d200c10 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 721531d2e9fd1e208a3fba8cfbe5dcd572599ca2
author iuc
date Tue, 05 Sep 2017 17:14:01 -0400
parents 2b3fac454f43
children bfe5103b1e8f
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0:2b3fac454f43 1:3dab7d200c10
10 @SHELL_OPTIONS@ 10 @SHELL_OPTIONS@
11 11
12 ## Symlinks creation or On the fly creation of a combo file 12 ## Symlinks creation or On the fly creation of a combo file
13 #if $input_type.type == 'list_collection' 13 #if $input_type.type == 'list_collection'
14 #for $pair in $input_type.list_paired_collection: 14 #for $pair in $input_type.list_paired_collection:
15 echo -e "${pair.name}\t${pair.forward}\t${pair.reverse}" >> combo_fastq.dat && 15 ln -s ${pair.forward} `basename ${pair.forward}` &&
16 ln -s ${pair.reverse} `basename ${pair.reverse}` &&
17 echo -e "${pair.name}\t`basename ${pair.forward}`\t`basename ${pair.reverse}`" >> combo_fastq.dat &&
16 #end for 18 #end for
17 #elif $input_type.type == 'simple_collection' 19 #elif $input_type.type == 'simple_collection'
18 ln -s '$input_type.paired_collection.forward' ffastq.dat && 20 ln -s '$input_type.paired_collection.forward' ffastq.dat &&
19 ln -s '$input_type.paired_collection.reverse' rfastq.dat && 21 ln -s '$input_type.paired_collection.reverse' rfastq.dat &&
20 #else 22 #else
175 <element name="reverse" value="Mock_S280_L001_R2_001_small.fastq" /> 177 <element name="reverse" value="Mock_S280_L001_R2_001_small.fastq" />
176 </collection> 178 </collection>
177 </element> 179 </element>
178 <element name="Pair2"> 180 <element name="Pair2">
179 <collection type="paired"> 181 <collection type="paired">
180 <element name="forward" value="Mock_S280_L001_R1_001_small.fastq" /> 182 <element name="forward" value="test_forward.fastq" />
181 <element name="reverse" value="Mock_S280_L001_R2_001_small.fastq" /> 183 <element name="reverse" value="test_reverse.fastq" />
182 </collection> 184 </collection>
183 </element> 185 </element>
184 </collection> 186 </collection>
185 </param> 187 </param>
186 </conditional> 188 </conditional>
187 <output name="fasta" md5="dab69a0e36f718b55d8defad26ec469b" ftype="fasta"/> 189 <output name="fasta" md5="91bd3b91adc6559182ad118b767f0a07" ftype="fasta"/>
188 <output name="qual" md5="cdba5409e4f87e3cd093a4e51084d616" ftype="qual"/> 190 <output name="qual" md5="7094d1ac82a40e9f89cc6cdf5e214da7" ftype="qual"/>
189 <output name="report" md5="80b992abd7e4d6a5e89fa70011ef2384" ftype="txt"/> 191 <output name="report" md5="96a07f664105e4ddcb645c7cd9f5d692" ftype="txt"/>
190 <output name="group" md5="2be2adb030c4fc001bfac7e1172b40e1" ftype="mothur.groups"/> 192 <output name="group" md5="ef83b393be4103f0b61a021234905210" ftype="mothur.groups"/>
191 <expand macro="logfile-test"/> 193 <expand macro="logfile-test"/>
192 </test> 194 </test>
193 </tests> 195 </tests>
194 <help> 196 <help>
195 <![CDATA[ 197 <![CDATA[