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comparison ribowaltz.xml @ 1:042cab870a39 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit 416063685092b818a398e00d5027f7fe742230f1
author iuc
date Mon, 23 Oct 2023 12:10:31 +0000
parents 6d4c94373bba
children
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0:6d4c94373bba 1:042cab870a39
1 <tool id="ribowaltz_process" name="riboWaltz" version="@VERSION@" profile="@PROFILE@"> 1 <tool id="ribowaltz_process" name="riboWaltz" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>calculation of optimal P-site offsets and diagnostic analysis</description> 2 <description>calculation of optimal P-site offsets and diagnostic analysis</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro='requirements'/>
7 <expand macro='edam_ontology' /> 6 <expand macro='edam_ontology' />
8 <expand macro='xrefs'/> 7 <expand macro='xrefs'/>
8 <expand macro='requirements'/>
9 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
10 #for $i, $sample in enumerate($rep_samples): 10 #for $i, $sample in enumerate($rep_samples):
11 ln -s $sample.bam_file $sample.sample_name'.bam' && 11 ln -s $sample.bam_file $sample.sample_name'.bam' &&
12 #end for 12 #end for
13 Rscript '${__tool_directory__}/ribowaltz.R' -b . -g '$gtf' --refseq_sep '$refseq_sep' 13 Rscript '${__tool_directory__}/ribowaltz.R' -b . -g '$gtf' --refseq_sep '$refseq_sep' --indel_threshold $indel_threshold
14 #import json 14 #import json
15 #if $filtering.duplicates.filter == 'yes': 15 #if $filtering.duplicates.filter == 'yes':
16 #set params_duplicate_filterting = [] 16 #set params_duplicate_filterting = []
17 #silent $params_duplicate_filterting.append({"extremity": str($filtering.duplicates.extremity), "keep": str($filtering.duplicates.keep)}) 17 #silent $params_duplicate_filterting.append({"extremity": str($filtering.duplicates.extremity), "keep": str($filtering.duplicates.keep)})
18 --params_duplicate_filterting '#echo json.dumps($params_duplicate_filterting)#' 18 --params_duplicate_filterting '#echo json.dumps($params_duplicate_filterting)#'
57 help="riboWaltz only works for read alignments based on transcript coordinates"/> 57 help="riboWaltz only works for read alignments based on transcript coordinates"/>
58 </repeat> 58 </repeat>
59 <param name="gtf" type="data" format="gtf,gff" label="Annotation in GTF format"/> 59 <param name="gtf" type="data" format="gtf,gff" label="Annotation in GTF format"/>
60 <param name="refseq_sep" type="text" optional="true" label="Separator between reference sequences' name and additional information to discard" 60 <param name="refseq_sep" type="text" optional="true" label="Separator between reference sequences' name and additional information to discard"
61 help=" All characters before the first occurrence of the specified separator are kept"/> 61 help=" All characters before the first occurrence of the specified separator are kept"/>
62 <param name="indel_threshold" type="integer" value="5" min="0"
63 label="Positive integer value specifying the maximum number of indels allowed for each read."/>
62 <param name="save_rdata" type="boolean" truevalue="1" falsevalue="0" checked="true" 64 <param name="save_rdata" type="boolean" truevalue="1" falsevalue="0" checked="true"
63 label="Save p-site info RDATA file?" 65 label="Save p-site info RDATA file?"
64 help="Useful for advanced plotting using riboWaltz-plot tool"/> 66 help="Useful for advanced plotting using riboWaltz-plot tool"/>
65 <section name="filtering" title="Filtering Options"> 67 <section name="filtering" title="Filtering Options">
66 <conditional name="duplicates"> 68 <conditional name="duplicates">
196 <assert_contents> 198 <assert_contents>
197 <has_size value="171803" delta="1000"/> 199 <has_size value="171803" delta="1000"/>
198 </assert_contents> 200 </assert_contents>
199 </output> 201 </output>
200 </test> 202 </test>
203 <test expect_num_outputs="5">
204 <param name="gtf" value="rep1_annot.gtf.gz"/>
205 <param name="refseq_sep" value="."/>
206 <param name="indel_threshold" value="3"/>
207 <param name="save_rdata" value="true"/>
208 <repeat name="rep_samples">
209 <param name="sample_name" value="Replicate1"/>
210 <param name="bam_file" value="rep1.bam"/>
211 </repeat>
212 <section name="filtering"/>
213 <section name="psite_additional">
214 <param name="flanking" value="3"/>
215 <param name="use_start" value="true"/>
216 <param name="psite_extrimity" value="auto"/>
217 <param name="cl" value="99"/>
218 </section>
219 <section name="coverage_additional">
220 <param name="psites_per_region" value="true"/>
221 <param name="min_overlap" value="1"/>
222 <param name="start_nts" value="0"/>
223 <param name="stop_nts" value="0"/>
224 </section>
225 <output name="codon_coverage_out">
226 <assert_contents>
227 <has_text_matching expression="transcript\tstart\tend\tfrom_cds_start\tfrom_cds_stop\tregion\tReplicate1"/>
228 <has_text_matching expression="ENSMUST00000000137\t2656\t2659\t865\t471\t3utr\t0"/>
229 </assert_contents>
230 </output>
231 <output name="cds_coverage_out">
232 <assert_contents>
233 <has_text_matching expression="transcript\tlength_cds\tReplicate1"/>
234 <has_text_matching expression="ENSMUST00000019109\t741\t5"/>
235 </assert_contents>
236 </output>
237 <output name="psite_rdata_out">
238 <assert_contents>
239 <has_size value="169141" delta="1000"/>
240 </assert_contents>
241 </output>
242 </test>
201 </tests> 243 </tests>
202 <help><![CDATA[ 244 <help><![CDATA[
203 riboWaltz is an R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data. Taking advantage of a two-step algorithm where offset information is passed through populations of reads with different length in order to maximize offset coherence, riboWaltz computes with high precision the P-site offset. riboWaltz also provides a variety of graphical representations, laying the foundations for further accurate RiboSeq analyses and improved interpretation of positional information. More information can be found here: https://github.com/LabTranslationalArchitectomics/riboWaltz 245 riboWaltz is an R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data. Taking advantage of a two-step algorithm where offset information is passed through populations of reads with different length in order to maximize offset coherence, riboWaltz computes with high precision the P-site offset. riboWaltz also provides a variety of graphical representations, laying the foundations for further accurate RiboSeq analyses and improved interpretation of positional information. More information can be found here: https://github.com/LabTranslationalArchitectomics/riboWaltz
204 246
205 **Inputs** 247 **Inputs**