Mercurial > repos > devteam > cuffquant
annotate cuffquant_wrapper.xml @ 4:679d93c99757 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffquant commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd"
author | iuc |
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date | Tue, 16 Jun 2020 13:01:50 -0400 |
parents | 6dc45faebc1d |
children | 93148c05136f |
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6dc45faebc1d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffquant commit 82ee6fc860c52c531b7a57bbb346ab1a67a434a5
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1 <tool id="cuffquant" name="Cuffquant" version="@VERSION@.1"> |
0 | 2 <!-- Wrapper supports Cuffdiff versions 2.2.1 --> |
3 <description>Precompute gene expression levels</description> | |
4 <macros> | |
5 <import>cuff_macros.xml</import> | |
6 </macros> | |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffquant commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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7 <expand macro="requirements" /> |
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679d93c99757
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffquant commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd"
iuc
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8 <version_command><![CDATA[cuffquant 2>&1 | head -n 1]]></version_command> |
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6dc45faebc1d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffquant commit 82ee6fc860c52c531b7a57bbb346ab1a67a434a5
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9 <command detect_errors="aggressive"><![CDATA[ |
0 | 10 cuffquant |
11 --no-update-check | |
12 --num-threads=\${GALAXY_SLOTS:-4} | |
13 ## Set advanced SE data parameters? | |
14 #if $additional.sAdditional == "Yes": | |
15 -m $additional.frag_mean_len | |
16 -s $additional.frag_len_std_dev | |
17 #end if | |
18 | |
19 ## Multi-read correct? | |
20 #if $multiread_correct : | |
21 -u | |
22 #end if | |
23 | |
24 ## Bias correction? | |
25 #if $bias_correction.do_bias_correction == "Yes": | |
26 -b | |
27 #if $bias_correction.seq_source.index_source == "history": | |
28 ## Custom genome from history. | |
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b2ee2bef1926
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffquant commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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29 '$bias_correction.seq_source.ref_file' |
0 | 30 #else: |
31 ## Built-in genome. | |
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b2ee2bef1926
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffquant commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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32 '${bias_correction.seq_source.index.fields.path}' |
0 | 33 #end if |
34 #end if | |
35 | |
36 $length_correction | |
37 | |
38 ## Set advanced parameters for cufflinks | |
39 #if $advanced_settings.sAdvanced == "Yes": | |
40 #if str($advanced_settings.library_type) != 'auto': | |
41 --library-type=$advanced_settings.library_type | |
42 #end if | |
43 #if $advanced_settings.mask_file: | |
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b2ee2bef1926
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffquant commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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44 --mask-file '$advanced_settings.mask_file' |
0 | 45 #end if |
46 --max-mle-iterations=$advanced_settings.max_mle_iterations | |
47 --max-bundle-frags=$advanced_settings.max_bundle_frags | |
48 #end if | |
49 ## Inputs. | |
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b2ee2bef1926
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffquant commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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50 '$gtf_input' |
0 | 51 #set samplestring = ','.join( [ str( $sample.sample ) for $sample in $samples ] ) |
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b2ee2bef1926
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffquant commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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52 '$samplestring' |
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6dc45faebc1d
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffquant commit 82ee6fc860c52c531b7a57bbb346ab1a67a434a5
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53 ]]></command> |
0 | 54 <inputs> |
55 <param format="gtf,gff3" name="gtf_input" type="data" label="Transcripts" | |
56 help="A transcript annotation (GFF3 or GTF) file produced by cufflinks, cuffcompare, or other source."/> | |
57 | |
58 <repeat name="samples" title="Replicate" min="1"> | |
59 <param name="sample" label="Add replicate" type="data" format="sam,bam"/> | |
60 </repeat> | |
61 | |
62 <param name="multiread_correct" type="boolean" label="Use multi-read correct" | |
63 help="Tells Cufflinks to do an initial estimation procedure to more accurately weight reads mapping to multiple locations in the genome." /> | |
64 | |
65 <conditional name="bias_correction"> | |
66 <param name="do_bias_correction" type="select" label="Perform Bias Correction" | |
67 help="Bias detection and correction can significantly improve accuracy of transcript abundance estimates."> | |
68 <option value="No">No</option> | |
69 <option value="Yes">Yes</option> | |
70 </param> | |
71 <when value="Yes"> | |
72 <conditional name="seq_source"> | |
73 <param name="index_source" type="select" label="Reference sequence data"> | |
74 <option value="cached">Locally cached</option> | |
75 <option value="history">History</option> | |
76 </param> | |
77 <when value="cached"> | |
78 <param name="index" type="select" label="Using reference genome"> | |
79 <options from_data_table="fasta_indexes"> | |
80 <filter type="data_meta" ref="gtf_input" key="dbkey" column="1" /> | |
81 <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" /> | |
82 </options> | |
83 </param> | |
84 </when> | |
85 <when value="history"> | |
86 <param name="ref_file" type="data" format="fasta" label="Using reference file" /> | |
87 </when> | |
88 </conditional> | |
89 </when> | |
90 <when value="No"></when> | |
91 </conditional> | |
92 | |
93 <param name="length_correction" type="select" label="apply length correction" help="mode of length normalization to transcript fpkm."> | |
94 <option value="" selected="true">cufflinks effective length correction</option> | |
95 <option value="--no-effective-length-correction">standard length correction</option> | |
96 <option value="--no-length-correction">no length correction at all (use raw counts)</option> | |
97 </param> | |
98 | |
99 <conditional name="additional"> | |
100 <param name="sAdditional" type="select" label="Set Additional Parameters for single end reads? (not recommended for paired-end reads)"> | |
101 <option value="No" selected="True">No</option> | |
102 <option value="Yes">Yes</option> | |
103 </param> | |
104 <when value="No"></when> | |
105 <when value="Yes"> | |
106 <param name="frag_mean_len" type="integer" value="200" label="Average Fragment Length"/> | |
107 <param name="frag_len_std_dev" type="integer" value="80" label="Fragment Length Standard Deviation"/> | |
108 </when> | |
109 </conditional> | |
110 | |
111 <conditional name="advanced_settings"> | |
112 <param name="sAdvanced" type="select" label="Set Advanced Cuffquant parameters? "> | |
113 <option value="No" selected="True">No</option> | |
114 <option value="Yes">Yes</option> | |
115 </param> | |
116 <when value="No"></when> | |
117 <when value="Yes"> | |
118 <param type="select" name="library_type" label="Library prep used for input reads" help=""> | |
119 <option value="auto" selected="True">Auto Detect</option> | |
120 <option value="ff-firststrand">ff-firststrand</option> | |
121 <option value="ff-secondstrand">ff-secondstrand</option> | |
122 <option value="ff-unstranded">ff-unstranded</option> | |
123 <option value="fr-firststrand">fr-firststrand</option> | |
124 <option value="fr-secondstrand">fr-secondstrand</option> | |
125 <option value="fr-unstranded" >fr-unstranded</option> | |
126 <option value="transfrags">transfrags</option> | |
127 </param> | |
128 <param name="mask_file" type="data" format="gtf,gff3" label="Mask File" help="Ignore all alignment within transcripts in this file" optional="True" /> | |
129 <param name="max_mle_iterations" value="5000" type="integer" label="Max MLE iterations" help="Maximum iterations allowed for Maximal Likelyhood Estimation calculations" /> | |
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986b63735a5e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffquant commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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130 <param name="max_bundle_frags" type="integer" value="500000" label="Maximum number of fragments per locus" |
0 | 131 help="Sets the maximum number of fragments a locus may have before being skipped. Default: 500,000" /> |
132 </when> | |
133 </conditional> | |
134 </inputs> | |
135 <outputs> | |
136 <!-- Standard datasets. --> | |
137 <data format="cxb" name="out_file" label="${tool.name} on ${on_string}: Abundances.cxb" from_work_dir="abundances.cxb" /> | |
138 </outputs> | |
139 <tests> | |
140 <test> | |
141 <!-- | |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffquant commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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142 cuffquant cuffcompare_out5.gtf cuffdiff_in1.sam,cuffdiff_in2.sam |
0 | 143 --> |
144 <param name="gtf_input" value="cuffquant_in.gtf" ftype="gtf" /> | |
145 <repeat name="samples"> | |
146 <param name="sample" value="cuffquant_in1.sam" ftype="sam" /> | |
147 </repeat> | |
148 <repeat name="samples"> | |
149 <param name="sample" value="cuffquant_in2.sam" ftype="sam" /> | |
150 </repeat> | |
151 <param name="length_correction" value="" /> | |
152 <param name="do_bias_correction" value="No" /> | |
153 <param name="multiread_correct" value="No"/> | |
154 <param name="sAdditional" value="No"/> | |
155 <param name="sAdvanced" value="No" /> | |
156 <output name="out_file" file="cuffquant_out1.cxb" compare="sim_size" /> | |
157 </test> | |
158 </tests> | |
159 | |
160 <help> | |
161 **Cuffquant Overview** | |
162 | |
163 Cuffquant is part of Cufflinks_. Cuffquant provides pre-calculation of gene expression levels. The resulting file can be provided to cuffdiff or cuffnorm for further processing. Please cite: Trapnell C, Williams BA, Pertea G, Mortazavi AM, Kwan G, van Baren MJ, Salzberg SL, Wold B, Pachter L. Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms. Nature Biotechnology doi:10.1038/nbt.1621 | |
164 | |
165 .. _Cufflinks: http://cole-trapnell-lab.github.io/cufflinks/ | |
166 | |
167 ------ | |
168 | |
169 **Know what you are doing** | |
170 | |
171 .. class:: warningmark | |
172 | |
173 There is no such thing (yet) as an automated gearshift in expression analysis. It is all like stick-shift driving in San Francisco. In other words, running this tool with default parameters will probably not give you meaningful results. A way to deal with this is to **understand** the parameters by carefully reading the `documentation`__ and experimenting. Fortunately, Galaxy makes experimenting easy. | |
174 | |
175 .. __: http://cole-trapnell-lab.github.io/cufflinks/cuffquant/ | |
176 | |
177 ------ | |
178 | |
179 **Input format** | |
180 | |
181 Cuffquant takes Cufflinks or Cuffcompare GTF files as input along with two or more SAM files containing the fragment alignments for two or more samples. | |
182 | |
183 ------ | |
184 | |
185 **Outputs** | |
186 | |
187 Cuffquant produces one output file: | |
188 | |
189 1. Transcript expression values in binary format. | |
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986b63735a5e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffquant commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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190 |
0 | 191 ------- |
192 | |
193 **Settings** | |
194 | |
195 All of the options have a default value. You can change any of them. Most of the options in Cuffdiff have been implemented here. | |
196 | |
197 ------ | |
198 | |
199 **Cuffdiff parameter list** | |
200 | |
201 This is a list of implemented Cuffdiff options:: | |
202 | |
203 -m INT Average fragment length (SE reads); default 200 | |
204 -s INT Fragment legnth standard deviation (SE reads); default 80 | |
205 --max-mle-iterations INT Sets the number of iterations allowed during maximum likelihood estimation of abundances. Default: 5000 | |
206 -u Multi read correction tells Cufflinks to do an initial estimation procedure to more accurately weight reads mapping to multiple locations in the genome. | |
207 -b ref.fasta bias correction. Bias detection and correction can significantly improve accuracy of transcript abundance estimates. | |
208 --no-effective-length-correction Use standard length correction | |
209 --no-length-correction Disable all length correction. | |
210 --library-type ff-firststrand,ff-secondstrand,ff-unstranded,fr-firstrand,fr-secondstrand,fr-unstranded,transfrags | |
211 --mask-file (gff3/gtf) Ignore all alignment within transcripts in this file | |
212 --max-bundle-frags Sets the maximum number of fragments a locus may have before being skipped. Skipped loci are listed in skipped.gtf. | |
213 </help> | |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffquant commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd"
iuc
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214 <expand macro="citations"/> |
0 | 215 </tool> |