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comparison cufflinks_wrapper.xml @ 12:d080005cffe1 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd"
author iuc
date Tue, 16 Jun 2020 13:00:32 -0400
parents e04dbae2abe0
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11:e04dbae2abe0 12:d080005cffe1
1 <tool id="cufflinks" name="Cufflinks" version="@VERSION@.2"> 1 <tool id="cufflinks" name="Cufflinks" version="@VERSION@.3">
2 <description>transcript assembly and FPKM (RPKM) estimates for RNA-Seq data</description> 2 <description>transcript assembly and FPKM (RPKM) estimates for RNA-Seq data</description>
3 <macros> 3 <macros>
4 <import>cuff_macros.xml</import> 4 <import>cuff_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements">
7 <version_command>cufflinks 2>&amp;1 | head -n 1</version_command> 7 <requirement type="package" version="3.6">python</requirement>
8 <command detect_errors="aggressive"> 8 </expand>
9 python '$__tool_directory__/cufflinks_wrapper.py' 9 <version_command><![CDATA[cufflinks 2>&1 | head -n 1]]></version_command>
10 --input '$input' 10 <command detect_errors="aggressive"><![CDATA[
11 --assembled-isoforms-output '$assembled_isoforms' 11 cufflinks -q --no-update-check
12 '$input'
12 --num-threads "\${GALAXY_SLOTS:-4}" 13 --num-threads "\${GALAXY_SLOTS:-4}"
13 -I $max_intron_len 14 -I $max_intron_len
14 -F $min_isoform_fraction 15 -F $min_isoform_fraction
15 -j $pre_mrna_fraction 16 -j $pre_mrna_fraction
16 $length_correction 17 $length_correction
29 30
30 ## Bias correction? 31 ## Bias correction?
31 #if $bias_correction.do_bias_correction == "Yes": 32 #if $bias_correction.do_bias_correction == "Yes":
32 -b 33 -b
33 #if $bias_correction.seq_source.index_source == "history": 34 #if $bias_correction.seq_source.index_source == "history":
34 --ref_file '$bias_correction.seq_source.ref_file' 35 '$bias_correction.seq_source.ref_file'
35 #else: 36 #else:
36 --index '${bias_correction.seq_source.index.fields.path}' 37 '${bias_correction.seq_source.index.fields.path}'
37 #end if 38 #end if
38 #end if 39 #end if
39 40
40 ## Multi-read correct? 41 ## Multi-read correct?
41 #if str($multiread_correct) == "Yes": 42 $multiread_correct
42 -u 43
43 #end if
44
45 ## Include global model if available.
46 #if $global_model:
47 --global_model '$global_model'
48 #end if
49
50 ## advanced settings 44 ## advanced settings
51 #if $advanced_settings.use_advanced_settings == "Yes": 45 #if $advanced_settings.use_advanced_settings == "Yes":
52 --library-type $advanced_settings.library_type 46 --library-type $advanced_settings.library_type
53 #if $advanced_settings.mask_file: 47 #if $advanced_settings.mask_file:
54 --mask-file '$advanced_settings.mask_file' 48 --mask-file '$advanced_settings.mask_file'
55 #end if 49 #end if
56 --inner-mean-dist $advanced_settings.inner_mean_dist 50 --frag-len-mean $advanced_settings.inner_mean_dist
57 --inner-dist-std-dev $advanced_settings.inner_dist_std_dev 51 --frag-len-std-dev $advanced_settings.inner_dist_std_dev
58 --max-mle-iterations $advanced_settings.max_mle_iterations 52 --max-mle-iterations $advanced_settings.max_mle_iterations
59 --junc-alpha $advanced_settings.junc_alpha 53 --junc-alpha $advanced_settings.junc_alpha
60 --small-anchor-fraction $advanced_settings.small_anchor_fraction 54 --small-anchor-fraction $advanced_settings.small_anchor_fraction
61 --overhang-tolerance $advanced_settings.overhang_tolerance 55 --overhang-tolerance $advanced_settings.overhang_tolerance
62 --max-bundle-length $advanced_settings.max_bundle_length 56 --max-bundle-length $advanced_settings.max_bundle_length
63 --max-bundle-frags $advanced_settings.max_bundle_frags 57 --max-bundle-frags $advanced_settings.max_bundle_frags
64 --min-intron-length $advanced_settings.min_intron_length 58 --min-intron-length $advanced_settings.min_intron_length
65 --trim-3-avgcov-thresh $advanced_settings.trim_three_avgcov_thresh 59 --trim-3-avgcov-thresh $advanced_settings.trim_three_avgcov_thresh
66 --trim-3-dropoff-frac $advanced_settings.trim_three_dropoff_frac 60 --trim-3-dropoff-frac $advanced_settings.trim_three_dropoff_frac
67 #end if 61 #end if
68 </command> 62 2> stderr
63
64 && python '$__tool_directory__/mass.py' stderr '$global_model' "transcripts.gtf"
65 ]]></command>
69 <inputs> 66 <inputs>
70 <param format="sam,bam" name="input" type="data" label="SAM or BAM file of aligned RNA-Seq reads" help=""/> 67 <param format="sam,bam" name="input" type="data" label="SAM or BAM file of aligned RNA-Seq reads" help=""/>
71 <param name="max_intron_len" type="integer" value="300000" min="1" max="600000" label="Max Intron Length" help="ignore alignments with gaps longer than this"/> 68 <param name="max_intron_len" type="integer" value="300000" min="1" max="600000" label="Max Intron Length" help="ignore alignments with gaps longer than this"/>
72 <param name="min_isoform_fraction" type="float" value="0.10" min="0" max="1" label="Min Isoform Fraction" help="suppress transcripts below this abundance level"/> 69 <param name="min_isoform_fraction" type="float" value="0.10" min="0" max="1" label="Min Isoform Fraction" help="suppress transcripts below this abundance level"/>
73 <param name="pre_mrna_fraction" type="float" value="0.15" min="0" max="1" label="Pre MRNA Fraction" help="suppress intra-intronic transcripts below this level"/> 70 <param name="pre_mrna_fraction" type="float" value="0.15" min="0" max="1" label="Pre MRNA Fraction" help="suppress intra-intronic transcripts below this level"/>
123 </conditional> 120 </conditional>
124 </when> 121 </when>
125 <when value="No" /> 122 <when value="No" />
126 </conditional> 123 </conditional>
127 124
128 <param name="multiread_correct" type="select" label="Use multi-read correct" 125 <param name="multiread_correct" type="boolean" label="Use multi-read correct"
129 help="Tells Cufflinks to do an initial estimation procedure to more accurately weight reads mapping to multiple locations in the genome."> 126 truevalue="-u" falsevalue="" checked="false"
130 <option value="No" selected="true">No</option> 127 help="Tells Cufflinks to do an initial estimation procedure to more accurately weight reads mapping to multiple locations in the genome."/>
131 <option value="Yes">Yes</option>
132 </param>
133 128
134 <param name="length_correction" type="select" label="Apply length correction" help="Mode of length normalization to transcript FPKM."> 129 <param name="length_correction" type="select" label="Apply length correction" help="Mode of length normalization to transcript FPKM.">
135 <option value="" selected="true">Cufflinks Effective Length Correction</option> 130 <option value="" selected="true">Cufflinks Effective Length Correction</option>
136 <option value="--no-effective-length-correction">Standard Length Correction</option> 131 <option value="--no-effective-length-correction">Standard Length Correction</option>
137 <option value="--no-length-correction">No Length Correction at all (use raw counts)</option> 132 <option value="--no-length-correction">No Length Correction at all (use raw counts)</option>
173 </conditional> 168 </conditional>
174 </inputs> 169 </inputs>
175 <outputs> 170 <outputs>
176 <data format="tabular" name="genes_expression" label="${tool.name} on ${on_string}: gene expression" from_work_dir="genes.fpkm_tracking"/> 171 <data format="tabular" name="genes_expression" label="${tool.name} on ${on_string}: gene expression" from_work_dir="genes.fpkm_tracking"/>
177 <data format="tabular" name="transcripts_expression" label="${tool.name} on ${on_string}: transcript expression" from_work_dir="isoforms.fpkm_tracking"/> 172 <data format="tabular" name="transcripts_expression" label="${tool.name} on ${on_string}: transcript expression" from_work_dir="isoforms.fpkm_tracking"/>
178 <data format="gtf" name="assembled_isoforms" label="${tool.name} on ${on_string}: assembled transcripts"/> 173 <data format="gtf" name="assembled_isoforms" label="${tool.name} on ${on_string}: assembled transcripts" from_work_dir="transcripts.gtf"/>
179 <data format="txt" name="total_map_mass" label="${tool.name} on ${on_string}: total map mass" hidden="true" from_work_dir="global_model.txt"/> 174 <data format="txt" name="total_map_mass" label="${tool.name} on ${on_string}: total map mass" hidden="true" from_work_dir="global_model.txt"/>
180 <data format="gtf" name="skipped" label="${tool.name} on ${on_string}: Skipped Transcripts" from_work_dir="skipped.gtf"/> 175 <data format="gtf" name="skipped" label="${tool.name} on ${on_string}: Skipped Transcripts" from_work_dir="skipped.gtf"/>
181 </outputs> 176 </outputs>
182 177
183 <trackster_conf> 178 <trackster_conf>
198 <param name="length_correction" value=""/> 193 <param name="length_correction" value=""/>
199 <param name="use_advanced_settings" value="No" /> 194 <param name="use_advanced_settings" value="No" />
200 <output name="genes_expression" ftype="tabular" lines_diff="2" file="cufflinks_out3.fpkm_tracking"/> 195 <output name="genes_expression" ftype="tabular" lines_diff="2" file="cufflinks_out3.fpkm_tracking"/>
201 <output name="transcripts_expression" ftype="tabular" lines_diff="2" file="cufflinks_out2.fpkm_tracking"/> 196 <output name="transcripts_expression" ftype="tabular" lines_diff="2" file="cufflinks_out2.fpkm_tracking"/>
202 <output name="assembled_isoforms" file="cufflinks_out1.gtf"/> 197 <output name="assembled_isoforms" file="cufflinks_out1.gtf"/>
203 <output name="global_model" file="cufflinks_out4.txt"/> 198 <output name="total_map_mass" file="cufflinks_out4.txt"/>
204 <output name="skipped" file="cufflinks_out4.gtf"/> 199 <output name="skipped" file="cufflinks_out4.gtf"/>
205 </test> 200 </test>
206 </tests> 201 </tests>
207 202
208 <help> 203 <help>
296 -F After calculating isoform abundance for a gene, Cufflinks filters out transcripts that it believes are very low abundance, because isoforms expressed at extremely low levels often cannot reliably be assembled, and may even be artifacts of incompletely spliced precursors of processed transcripts. This parameter is also used to filter out introns that have far fewer spliced alignments supporting them. The default is 0.05, or 5% of the most abundant isoform (the major isoform) of the gene. 291 -F After calculating isoform abundance for a gene, Cufflinks filters out transcripts that it believes are very low abundance, because isoforms expressed at extremely low levels often cannot reliably be assembled, and may even be artifacts of incompletely spliced precursors of processed transcripts. This parameter is also used to filter out introns that have far fewer spliced alignments supporting them. The default is 0.05, or 5% of the most abundant isoform (the major isoform) of the gene.
297 -j Some RNA-Seq protocols produce a significant amount of reads that originate from incompletely spliced transcripts, and these reads can confound the assembly of fully spliced mRNAs. Cufflinks uses this parameter to filter out alignments that lie within the intronic intervals implied by the spliced alignments. The minimum depth of coverage in the intronic region covered by the alignment is divided by the number of spliced reads, and if the result is lower than this parameter value, the intronic alignments are ignored. The default is 5%. 292 -j Some RNA-Seq protocols produce a significant amount of reads that originate from incompletely spliced transcripts, and these reads can confound the assembly of fully spliced mRNAs. Cufflinks uses this parameter to filter out alignments that lie within the intronic intervals implied by the spliced alignments. The minimum depth of coverage in the intronic region covered by the alignment is divided by the number of spliced reads, and if the result is lower than this parameter value, the intronic alignments are ignored. The default is 5%.
298 -G Tells Cufflinks to use the supplied reference annotation to estimate isoform expression. It will not assemble novel transcripts, and the program will ignore alignments not structurally compatible with any reference transcript. 293 -G Tells Cufflinks to use the supplied reference annotation to estimate isoform expression. It will not assemble novel transcripts, and the program will ignore alignments not structurally compatible with any reference transcript.
299 -N With this option, Cufflinks excludes the contribution of the top 25 percent most highly expressed genes from the number of mapped fragments used in the FPKM denominator. This can improve robustness of differential expression calls for less abundant genes and transcripts. 294 -N With this option, Cufflinks excludes the contribution of the top 25 percent most highly expressed genes from the number of mapped fragments used in the FPKM denominator. This can improve robustness of differential expression calls for less abundant genes and transcripts.
300 </help> 295 </help>
301 <citations> 296 <expand macro="citations"/>
302 <citation type="doi">10.1038/nbt.1621</citation>
303 </citations>
304 </tool> 297 </tool>