Mercurial > repos > dnbenso > masurca

comparison masurca.xml @ 3:784cb0a6cfdb draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author dnbenso
date Fri, 28 Jan 2022 04:20:09 +0000
parents 1808eaa9d699
children
comparison
equal deleted inserted replaced
2:1808eaa9d699 3:784cb0a6cfdb
8 </requirements> 8 </requirements>
9 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
10 cp $__tool_directory__/default-masurca-config config.txt && 10 cp $__tool_directory__/default-masurca-config config.txt &&
11 #if $nanopore_input.np_input == "Yes": 11 #if $nanopore_input.np_input == "Yes":
12 #if $pacbio_input.pb_input == "Yes": 12 #if $pacbio_input.pb_input == "Yes":
13 cat '$nanopore_input.nano' '$pacbio_input.pacbio' > long.fastq.gz && 13 cat '$nanopore_input.nano' '$pacbio_input.pacbio' > \$_GALAXY_JOB_TMP_DIR/long.fastq.gz &&
14 #else: 14 #else:
15 ln -s '$nanopore_input.nano' long.fastq.gz && 15 ln -s '$nanopore_input.nano' \$_GALAXY_JOB_TMP_DIR/long.fastq.gz &&
16 #end if 16 #end if
17 sed -i 's|#NANOPORE=INPUTREADLONG|NANOPORE=long.fastq.gz|' config.txt && 17 sed -i 's|#NANOPORE=INPUTREADLONG|NANOPORE='\$_GALAXY_JOB_TMP_DIR'/long.fastq.gz|' config.txt &&
18 #elif $pacbio_input.pb_input == "Yes": 18 #elif $pacbio_input.pb_input == "Yes":
19 ln -s '$pacbio_input.pacbio' long.fastq.gz && 19 ln -s '$pacbio_input.pacbio' \$_GALAXY_JOB_TMP_DIR/long.fastq.gz &&
20 sed -i 's|#PACBIO=INPUTREADLONG|PACBIO=long.fastq.gz|' config.txt && 20 sed -i 's|#PACBIO=INPUTREADLONG|PACBIO='\$_GALAXY_JOB_TMP_DIR'/long.fastq.gz|' config.txt &&
21 #end if 21 #end if
22 #if str( $illumina_input.input_type ) == "single" 22 #if str( $illumina_input.input_type ) == "single"
23 ln -s '$illumina_input.fastq_input1' ill_1.fastq.gz && 23 ln -s '$illumina_input.fastq_input1' ill_1.fastq.gz &&
24 sed -i 's|INPUTREAD1|ill_1.fastq.gz|' config.txt && 24 sed -i 's|INPUTREAD1|ill_1.fastq.gz|' config.txt &&
25 #elif str( $illumina_input.input_type ) == "paired" 25 #elif str( $illumina_input.input_type ) == "paired"
117 <filter>flye == False</filter> 117 <filter>flye == False</filter>
118 </data> 118 </data>
119 <data name="flye_assembly" format="fasta" from_work_dir="flye.mr.*/assembly.fasta" label="${tool.name} on ${on_string}: flye_assembly"> 119 <data name="flye_assembly" format="fasta" from_work_dir="flye.mr.*/assembly.fasta" label="${tool.name} on ${on_string}: flye_assembly">
120 <filter>flye == True</filter> 120 <filter>flye == True</filter>
121 </data> 121 </data>
122 <data name="flye_log" format="txt" from_work_dir="flye.mr.*/flye.log" label="${tool.name} on ${on_string}: flye_log">
123 <filter>flye == True</filter>
124 </data>
122 </outputs> 125 </outputs>
123 <tests> 126 <tests>
124 <test> 127 <test>
125 <!-- 128 <!--
126 The test files are too large for upload to a toolshed or git repo. 129 The test files are too large for upload to a toolshed or git repo.
169 172
170 ----- 173 -----
171 174
172 **Input data** 175 **Input data**
173 176
174 The following types of data are supported:: 177 The following types of data are supported:
175 178
176 * Illumina paired end (or single end) reads -- MANDATORY. The mean and stdev parameters are the library insert average length and standard deviation. If the standard deviation is not known, set it to approximately 15% of the mean.If the second (reverse) read set is not available, do not specify it and just specify the forward reads. Files must be in fastq format and can be gzipped. 179 * Illumina paired end (or single end) reads -- MANDATORY. The mean and stdev parameters are the library insert average length and standard deviation. If the standard deviation is not known, set it to approximately 15% of the mean.If the second (reverse) read set is not available, do not specify it and just specify the forward reads. Files must be in fastq format and can be gzipped.
177 * PacBio/MinION data are supported. Note that you have to have 50x + coverage in Illumina Paired End reads to use PacBio of Oxford Nanopore MinION data. Supply PacBio or MinION reads in a single fasta or fastq file (can be gzipped). 180 * PacBio/MinION data are supported. Note that you have to have 50x + coverage in Illumina Paired End reads to use PacBio of Oxford Nanopore MinION data. Supply PacBio or MinION reads in a single fasta or fastq file (can be gzipped).
178 181
179 **Parameters** 182 **Parameters**
180 183
181 The following parameter is mandatory:: 184 The following parameter is mandatory:
182 185
183 * jellyfish hash size, set this to about 10x the genome size. 186 * jellyfish hash size, set this to about 10x the genome size.
184 187
185 Optional parameters: 188 Optional parameters:
186 189