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comparison mircounts.xml @ 1:cadc0f2c6b29 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit b403f95dd2e57e51932fa275bdaed5312ffc1ff1
author artbio
date Tue, 25 Jul 2017 09:40:25 -0400
parents da29af78a960
children f59c643b00fc
comparison
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0:da29af78a960 1:cadc0f2c6b29
1 <tool id="mircounts" name="miRcounts" version="0.9"> 1 <tool id="mircounts" name="miRcounts" version="0.9.1">
2 <description> Counts miRNA alignments from small RNA sequence data</description> 2 <description> Counts miRNA alignments from small RNA sequence data</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.2">bowtie</requirement> 4 <requirement type="package" version="1.2">bowtie</requirement>
5 <requirement type="package" version="1.4.1">samtools</requirement> 5 <requirement type="package" version="1.4.1">samtools</requirement>
6 <requirement type="package" version="0.11.2.1">pysam</requirement> 6 <requirement type="package" version="0.11.2.1">pysam</requirement>
157 </test> 157 </test>
158 </tests> 158 </tests>
159 <help> 159 <help>
160 160
161 **What it does** 161 **What it does**
162 Clip adapter (optional), align small RNA read to miRNA mirBase_ reference using bowtie and compute pre-mir and mir counts using the pysam python package. 162
163 Optionally, pre-mir read coverages can be plotted using the R lattice package. 163 + Clips adapter (optional)
164 + Aligns small RNA reads to miRNA mirBase_ reference using bowtie
165 + Computes pre-mir and mir counts using the pysam python package
166 + Plots pre-mir read coverages using R lattice package (optional)
167
164 This tool uses a species-specific GFF3 file generated from mirBase_ to guide the parsing of a bam file of small RNA alignments. 168 This tool uses a species-specific GFF3 file generated from mirBase_ to guide the parsing of a bam file of small RNA alignments.
165 169
166 .. _mirBase: ftp://mirbase.org/pub/mirbase/CURRENT/genomes/ 170 .. _mirBase: ftp://mirbase.org/pub/mirbase/CURRENT/genomes/
167 171
168 ------ 172 ------
169 173
170 174
171 **Inputs** 175 **Inputs**
172 176
173 1. a fastq file of reads that may or may not clipped from their adapter sequence. The tool includes a clipping option if needed. 177 1. A fastq file of reads that may or may not be clipped from their adapter sequence. The tool includes a clipping option if needed.
174 178 2. Select the appropriate organism which reads originate from.
175 2. select the appropriate organism from which reads originate 179 3. Choose whether you wish or not to plot the pre-mir coverages. The coverage can be expressed in absolute number of reads covering the real coordinates of the pre-mir sequences, or, as a fraction of the maximum coverage (set to 1) covering the coordinates of pre-mirs expressed as a fraction of the length of the pre-mirs.
176 180
177 3. Choose whether you wish or not to plot the pre-mir coverages
178 Coverage can be expressed in absolute number of reads covering the real coordinates of the pre-mir sequences,
179 or, in fraction of reads relative to the maximum coverage (set to 1) covering the coordinates of pre-mirs
180 expressed as a fraction of the length of the pre-mirs.
181 181
182 ------ 182 ------
183 183
184 Absolute :
185
186 + .. image:: premirs_absolute.png
187
188 Relative :
189
190 + .. image:: premirs_relative.png
191
192 -------
193
184 **Outputs** 194 **Outputs**
185 195
186 1. a BAM alignment of input reads 196 1. A BAM alignment of input reads
187 2. a gff3 file generated by the tool to compute mature mir counts 197 2. A GFF3 file generated by the tool to compute mature mir counts
188 3 a table of pre-mir Counts 198 3. A table of pre-mir counts
189 4 a table of mature mir Counts 199 4. A table of mature mir counts
190 200
191 Optional: 201 Optional:
202
192 5. A table of pre-mir coverage 203 5. A table of pre-mir coverage
193 6. A pdf file with covererage plots 204 6. A PDF file with covererage plots
205
194 206
195 </help> 207 </help>
196 <citations> 208 <citations>
197 <citation type="doi">10.1093/bioinformatics/btp352</citation> 209 <citation type="doi">10.1093/bioinformatics/btp352</citation>
198 <citation type="doi">10.1186/gb-2009-10-3-r25</citation> 210 <citation type="doi">10.1186/gb-2009-10-3-r25</citation>