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comparison scpipe.xml @ 1:4ec6717872b1 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit ffcc4ba8dcf01fd19bee6d946f9789bcf4ed680a
author iuc
date Fri, 17 Aug 2018 08:22:49 -0400
parents 32e1bfc6b7b2
children 5c4bca9dd4a2
comparison
equal deleted inserted replaced
0:32e1bfc6b7b2 1:4ec6717872b1
26 26
27 #if $ref_fasta.fasta_source == "history": 27 #if $ref_fasta.fasta_source == "history":
28 #set $fasta_name = re.sub('[^\w\-\s]', '_', str($ref_fasta.ref_fa_hist.element_identifier)) 28 #set $fasta_name = re.sub('[^\w\-\s]', '_', str($ref_fasta.ref_fa_hist.element_identifier))
29 ln -s '$ref_fasta.ref_fa_hist' '$fasta_name' && 29 ln -s '$ref_fasta.ref_fa_hist' '$fasta_name' &&
30 #else: 30 #else:
31 #set $fasta_name = re.sub('[^\w\-\s]', '_', str($ref_fasta.ref_fa_builtin.element_identifier)) 31 #set $fasta_name = os.path.basename(str($ref_fasta.ref_fa_builtin.fields.path))
32 ln -s '$ref_fasta.ref_fa_builtin.fields.path' '$fasta_name' && 32 ln -s '$ref_fasta.ref_fa_builtin.fields.path' '$fasta_name' &&
33 #end if 33 #end if
34 34
35 #set $anno_name = re.sub('[^\w\-\s]', '_', str($exons.element_identifier)) 35 #set $anno_name = re.sub('[^\w\-\s]', '_', str($exons.element_identifier))
36 #set $anno_name = $anno_name + ".gff3" 36 #set $anno_name = $anno_name + ".gff3"
154 <param name="rscript" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="Output Rscript?" help="If this option is set to Yes, the Rscript used to annotate the IDs will be provided as a text file in the output. Default: No" /> 154 <param name="rscript" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="Output Rscript?" help="If this option is set to Yes, the Rscript used to annotate the IDs will be provided as a text file in the output. Default: No" />
155 <param name="rdata" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output RData file?" 155 <param name="rdata" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output RData file?"
156 help="Output all the data used by R to construct the tables and plots, can be loaded into R. Default: No"> 156 help="Output all the data used by R to construct the tables and plots, can be loaded into R. Default: No">
157 </param> 157 </param>
158 <section name="adv" title="Advanced Options"> 158 <section name="adv" title="Advanced Options">
159 <param argument="--rmlow" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Remove reads with N in barcode or UMI. Default: Yes" /> 159 <param argument="--rmlow" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Remove reads with N in barcode or UMI" help="Default: Yes" />
160 <param argument="--rmN" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Remove reads with low quality. Default: Yes" /> 160 <param argument="--rmN" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Remove reads with low quality" help="Default: Yes" />
161 <param argument="--minq" type="integer" min="0" value="20" label="Minimum read quality. Default: 20" /> 161 <param argument="--minq" type="integer" min="0" value="20" label="Minimum read quality" help="Default: 20" />
162 <param argument="--numbq" type="integer" min="0" value="2" label="Maximum number of bases below minq. Default: 2" /> 162 <param argument="--numbq" type="integer" min="0" value="2" label="Maximum number of bases below minq" help="Default: 2" />
163 <param argument="--stnd" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Perform strand-specific mapping. Default: Yes" /> 163 <param argument="--stnd" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Perform strand-specific mapping" help="Default: Yes" />
164 <param argument="--max_mis" type="integer" min="0" value="1" label="Maximum mismatch allowed in barcode. Default: 1" /> 164 <param argument="--max_mis" type="integer" min="0" value="1" label="Maximum mismatch allowed in barcode" help="Default: 1" />
165 <param argument="--UMI_cor" type="integer" min="0" value="1" label="Correct UMI sequence error" help="0 means no correction, 1 means simple correction and merge UMI with distance 1. Default: 1" /> 165 <param argument="--UMI_cor" type="integer" min="0" value="1" label="Correct UMI sequence error" help="0 means no correction, 1 means simple correction and merge UMI with distance 1. Default: 1" />
166 <param argument="--gene_fl" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Remove low abundant genes" help="Low abundant is defined as only one copy of one UMI for this gene. Default: No" /> 166 <param argument="--gene_fl" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Remove low abundant genes" help="Low abundant is defined as only one copy of one UMI for this gene. Default: No" />
167 <param argument="--max_reads" type="integer" min="0" value="1000000" label="Maximum reads processed" help="Maximum reads processed if detecting barcodes. Default: 1,000,000" /> 167 <param argument="--max_reads" type="integer" min="0" value="1000000" label="Maximum reads processed" help="Maximum reads processed if detecting barcodes. Default: 1,000,000" />
168 <param argument="--min_count" type="integer" min="0" value="10" label="Minimum count to keep" help="Minimum count to keep if detecting barcodes. Barcode will be discarded if it has lower count. This should be set according to --max_reads. Default: 10" /> 168 <param argument="--min_count" type="integer" min="0" value="10" label="Minimum count to keep" help="Minimum count to keep if detecting barcodes. Barcode will be discarded if it has lower count. This should be set according to --max_reads. Default: 10" />
169 </section> 169 </section>
204 <assert_contents> 204 <assert_contents>
205 <has_text text="scPipe report for sample" /> 205 <has_text text="scPipe report for sample" />
206 </assert_contents> 206 </assert_contents>
207 </output> 207 </output>
208 </test> 208 </test>
209 <!-- Ensure built-in fasta works -->
210 <test>
211 <param name="fasta_source" value="cached"/>
212 <param name="exons" ftype="gff3" value="mm10_MT19.gff3.gz"/>
213 <param name="paired_format_selector" value="paired" />
214 <param name="in1" ftype="fastqsanger.gz" dbkey="mm10" value="CB51_MT19_R1.gz"/>
215 <param name="in2" ftype="fastqsanger.gz" dbkey="mm10" value="CB51_MT19_R2.gz"/>
216 <param name="us" value="-1"/>
217 <param name="max_reads" value="5000000"/>
218 <param name="min_count" value="100"/>
219 <param name="report" value="False" />
220 <output name="out_matrix" >
221 <assert_contents>
222 <has_text text="ENSMUSG00000064351" />
223 </assert_contents>
224 </output>
225 </test>
209 </tests> 226 </tests>
210 <help><![CDATA[ 227 <help><![CDATA[
211 .. class:: infomark 228 .. class:: infomark
212 229
213 **What it does** 230 **What it does**