comparison make_EAR.xml @ 0:8c99976de71e draft

planemo upload for repository https://github.com/ERGA-consortium/EARs/tree/main commit e9db2e88e55a442d7f8fdb5e8e86330410d2e92d
author bgruening
date Fri, 07 Jun 2024 14:23:49 +0000
parents
children b61022e1b807
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-1:000000000000 0:8c99976de71e
1 <tool id="make_ear" name="ERGA Assembly Reporting Tool (EAR)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
2 <description>A tool to compile assembly reports and stastics from assembly pipeline</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <requirements>
7 <requirement type="package" version="4.1.0">reportlab</requirement>
8 <requirement type="package" version="24.4.0">pyaml</requirement>
9 <requirement type="package" version="2024.1">pytz</requirement>
10 <requirement type="package" version="2.32.3">requests</requirement>
11 </requirements>
12 <command detect_errors="exit_code"><![CDATA[
13 python '$__tool_directory__/make_EAR.py' '$param_file' > '$log'
14 ]]></command>
15 <configfiles>
16 <configfile name="param_file"><![CDATA[
17 # SAMPLE INFORMATION
18 ToLID: '${sample_information.tolid}'
19 Species: '${sample_information.species_name}'
20 Sex: '${sample_information.species_sex}'
21 Submitter: '${sample_information.submitter}'
22 Affiliation: '${sample_information.affiliation}'
23 Tags: '${sample_information.tags}'
24
25 # SEQUENCING DATA
26 DATA:
27 #for $repeat in $sequencing_data.seq_data_info:
28 - ${repeat.seq_data}
29 #end for
30
31 # GENOME PROFILING DATA
32 PROFILING:
33 GenomeScope:
34 genomescope_summary_txt: '${genome_profiling_data.genome_scope_summary}'
35 Smudgeplot:
36 smudgeplot_verbose_summary_txt: '${genome_profiling_data.smudge_plot_summary}'
37
38 #if $pre_curation_assembly_data.hap2_precuration_data.hap2_exists_precuration == "yes"
39 # ASSEMBLY DATA
40 ASSEMBLIES:
41 Pre-curation:
42 pipeline: [Hifiasm_v0.19.4|HiC|l0, Purge_Dups_v1.2.6|, Bionano_vGalaxy_3.7.0, YaHS_v1.1]
43 '${pre_curation_assembly_data.haplotype_selection}':
44 gfastats--nstar-report_txt: '${pre_curation_assembly_data.gfstats_nstar_report_precuration}'
45 busco_short_summary_txt: '${pre_curation_assembly_data.busco_short_summary_precuration}'
46 merqury_qv: '${pre_curation_assembly_data.mercury_qv_precuration}'
47 merqury_completeness_stats: '${pre_curation_assembly_data.merqury_completeness_stats_precuration}'
48 hap2:
49 gfastats--nstar-report_txt: '${pre_curation_assembly_data.hap2_precuration_data.gfstats_nstar_report_hap2_precuration}'
50 busco_short_summary_txt: '${pre_curation_assembly_data.hap2_precuration_data.busco_short_summary_hap2_precuration}'
51 merqury_qv: '${pre_curation_assembly_data.hap2_precuration_data.mercury_qv_hap2_precuration}'
52 merqury_completeness_stats: '${pre_curation_assembly_data.hap2_precuration_data.merqury_completeness_stats_hap2_precuration}'
53
54 Curated:
55 pipeline: [GRIT_rapid_v2.0, HiGlass_v1.0]
56 '${pre_curation_assembly_data.haplotype_selection}':
57 gfastats--nstar-report_txt: '${curated_assembly_data.gfstats_nstar_report_curated}'
58 busco_short_summary_txt: '${curated_assembly_data.busco_short_summary_curated}'
59 merqury_qv: '${curated_assembly_data.mercury_qv_curated}'
60 merqury_completeness_stats: '${curated_assembly_data.merqury_completeness_stats_curated}'
61 merqury_hap_spectra_cn_png: '${curated_assembly_data.merqury_hap_spectra_cn_curated}'
62 merqury_spectra_cn_png: '${curated_assembly_data.merqury_spectra_cn_curated}'
63 merqury_spectra_asm_png: '${curated_assembly_data.merqury_spectra_asm_curated}'
64 hic_FullMap_png: '${curated_assembly_data.hic_FullMap_curated}'
65 hic_FullMap_link: '${curated_assembly_data.hic_FullMap_link_curated}'
66 blobplot_cont_png: '${curated_assembly_data.blobplot_cont_curated}'
67 hap2:
68 gfastats--nstar-report_txt: '${curated_assembly_data.hap2_curated_data.gfstats_nstar_report_hap2_curated}'
69 busco_short_summary_txt: '${curated_assembly_data.hap2_curated_data.busco_short_summary_hap2_curated}'
70 merqury_qv: '${curated_assembly_data.hap2_curated_data.mercury_qv_hap2_curated}'
71 merqury_completeness_stats: '${curated_assembly_data.hap2_curated_data.merqury_completeness_stats_hap2_curated}'
72 merqury_hap_spectra_cn_png: '${curated_assembly_data.hap2_curated_data.merqury_hap_spectra_cn_hap2_curated}'
73 merqury_spectra_cn_png: '${curated_assembly_data.hap2_curated_data.merqury_spectra_cn_hap2_curated}'
74 merqury_spectra_asm_png: '${curated_assembly_data.hap2_curated_data.merqury_spectra_asm_hap2_curated}'
75 hic_FullMap_png: '${curated_assembly_data.hap2_curated_data.hic_FullMap_hap2_curated}'
76 hic_FullMap_link: '${curated_assembly_data.hap2_curated_data.hic_FullMap_link_hap2_curated}'
77 blobplot_cont_png: '${curated_assembly_data.hap2_curated_data.blobplot_cont_hap2_curated}'
78
79 #else
80 # ASSEMBLY DATA
81 ASSEMBLIES:
82 Pre-curation:
83 pipeline: [Hifiasm_v0.19.4|HiC|l0, Purge_Dups_v1.2.6|, Bionano_vGalaxy_3.7.0, YaHS_v1.1]
84 '${pre_curation_assembly_data.haplotype_selection}':
85 gfastats--nstar-report_txt: '${pre_curation_assembly_data.gfstats_nstar_report_precuration}'
86 busco_short_summary_txt: '${pre_curation_assembly_data.busco_short_summary_precuration}'
87 merqury_qv: '${pre_curation_assembly_data.mercury_qv_precuration}'
88 merqury_completeness_stats: '${pre_curation_assembly_data.merqury_completeness_stats_precuration}'
89
90 Curated:
91 pipeline: [GRIT_rapid_v2.0, HiGlass_v1.0]
92 '${pre_curation_assembly_data.haplotype_selection}':
93 gfastats--nstar-report_txt: '${curated_assembly_data.gfstats_nstar_report_curated}'
94 busco_short_summary_txt: '${curated_assembly_data.busco_short_summary_curated}'
95 merqury_qv: '${curated_assembly_data.mercury_qv_curated}'
96 merqury_completeness_stats: '${curated_assembly_data.merqury_completeness_stats_curated}'
97 merqury_hap_spectra_cn_png: '${curated_assembly_data.merqury_hap_spectra_cn_curated}'
98 merqury_spectra_cn_png: '${curated_assembly_data.merqury_spectra_cn_curated}'
99 merqury_spectra_asm_png: '${curated_assembly_data.merqury_spectra_asm_curated}'
100 hic_FullMap_png: '${curated_assembly_data.hic_FullMap_curated}'
101 hic_FullMap_link: '${curated_assembly_data.hic_FullMap_link_curated}'
102 blobplot_cont_png: '${curated_assembly_data.blobplot_cont_curated}'
103 #end if
104
105 # CURATION NOTES
106 NOTES:
107 Obs_Haploid_num: '${curation_notes.obs_haploid_num}'
108 Obs_Sex: '${curation_notes.obs_sex}'
109 Interventions_per_Gb: '${curation_notes.interventions_per_gb}'
110 Contamination_notes: '${curation_notes.contam_notes}'
111 Other_notes: '${curation_notes.other_notes}'
112
113 ]]></configfile>
114 </configfiles>
115
116 <inputs>
117 <!-- Input parameters for Sample Information -->
118 <section name="sample_information" title="Sample Information" expanded="true">
119 <param name="tolid" type="text" optional="False" value="" label="Input a ToLID"/>
120 <param name="species_name" type="text" optional="False" value="" label="Enter the Species name"/>
121 <param name="species_sex" type="select" label="Enter the Species sex">
122 <option value="XX">XX</option>
123 <option value="XY">XY</option>
124 <option value="X0">X0</option>
125 <option value="ZZ">ZZ</option>
126 <option value="ZW">ZW</option>
127 <option value="NA">Not Available</option>
128 </param>
129 <param name="submitter" type="text" value="" optional="False" label="Enter the Submitter name"/>
130 <param name="affiliation" type="text" value="" optional="False" label="Enter the Affiliation"/>
131 <param name="tags" type="select" label="Select a valid tag">
132 <option value="ERGA-BGE" selected="true">ERGA-BGE</option>
133 <option value="ERGA-Pilot">ERGA-Pilot</option>
134 <option value="ERGA-Satellite">ERGA-Satellite</option>
135 </param>
136 </section>
137
138 <!-- Input parameters for Sequence Data Information -->
139 <section name="sequencing_data" title="Sequencing Data Information">
140 <repeat name='seq_data_info' title="Add Sequence Data information" min="1" default="2">
141 <param name="seq_data" type="text" label="Enter Sequencing data information" optional="False" help="Input Sequencing data information along with coverage scores if available. (Example Input: HiFi: 40X)"/>
142 </repeat>
143 </section>
144
145 <!-- Input parameters for Genome Profiling Data -->
146 <section name="genome_profiling_data" title="Genome Profiling Information">
147 <param name="genome_scope_summary" type="data" format="txt" label="Summary file from GenomeScope tool"/>
148 <param name="smudge_plot_summary" type="data" format="txt" optional="true" label="Summary file from Smudge Plot tool"/>
149 </section>
150
151 <!-- Input parameters for Assembly data precurated -->
152 <section name="pre_curation_assembly_data" title="Pre-Curation Assembly Information">
153 <param name="pipeline_tools_precuration" type="text" label="Input tool names along with version and paramters used" help="[Insert ToolA_v1.2.3|ParamX|ParamY, Insert ToolB_v2.3.4] valid input is empty or between brackets ToolName followed by _v followed by versionNumber followed by | followed by keyToolParameter"/>
154 <param name="haplotype_selection" type="select" label="Select a valid haplotype">
155 <option value="hap1">hap1</option>
156 <option value="pri">pri</option>
157 <option value="collapsed">collapsed</option>
158 </param>
159 <param name="gfstats_nstar_report_precuration" type="data" format="txt" label="Select gfastats--nstar report file from gfstats tool"/>
160 <param name="busco_short_summary_precuration" type="data" format="txt" label="Select short summary report file from busco tool"/>
161 <param name="mercury_qv_precuration" type="data" format="txt" label="Select Merqury results .qv file"/>
162 <param name="merqury_completeness_stats_precuration" type="data" format="txt" label="Select Merqury results completeness.stats file"/>
163 <conditional name="hap2_precuration_data">
164 <param name="hap2_exists_precuration" type="select" label="Do you have data for Hap2?">
165 <option value="no" selected="true">No</option>
166 <option value="yes">Yes</option>
167 </param>
168 <when value="no"/>
169 <when value="yes">
170 <param name="gfstats_nstar_report_hap2_precuration" type="data" format="data" label="Select gfastats--nstar report tool from gfstats tool for Hap2"/>
171 <param name="busco_short_summary_hap2_precuration" type="data" format="txt" label="Select short summary from busco tool for Hap2"/>
172 <param name="mercury_qv_hap2_precuration" type="data" format="txt" label="Select Merqury results .qv file for Hap2"/>
173 <param name="merqury_completeness_stats_hap2_precuration" type="data" format="txt" label="Select Merqury results completeness.stats file for Hap2"/>
174 </when>
175 </conditional>
176 </section>
177
178 <!-- Input parameters for Assembly data Curated -->
179 <section name="curated_assembly_data" title="Curated Assembly Data Information">
180 <param name="pipeline_tools_curation" type="text" label="Input tool names along with version and paramters used" help="[Insert ToolA_v1.2.3|ParamX|ParamY, Insert ToolB_v2.3.4] valid input is empty or between brackets ToolName followed by _v followed by versionNumber followed by | followed by keyToolParameter"/>
181 <param name="gfstats_nstar_report_curated" type="data" format="txt" label="Select curated gfastats--nstar report file"/>
182 <param name="busco_short_summary_curated" type="data" format="txt" label="Select curated busco_short_summary.txt file"/>
183 <param name="mercury_qv_curated" type="data" format="txt" label="Select curated Merqury results .qv file"/>
184 <param name="merqury_completeness_stats_curated" type="data" format="txt" label="Select curated Merqury completeness.stats file"/>
185 <param name="merqury_hap_spectra_cn_curated" type="data" format="png" label="Select Merqury HAP1 spectra-cn.ln.png file"/>
186 <param name="merqury_spectra_cn_curated" type="data" format="png" label="Select Merqury results spectra-cn.ln.png file"/>
187 <param name="merqury_spectra_asm_curated" type="data" format="png" label="Select Merqury results spectra-asm.ln.png file"/>
188 <param name="hic_FullMap_curated" type="data" format="png" label="Select pretext FullMap plot"/>
189 <param name="hic_FullMap_link_curated" type="text" value="" label="Insert .pretext file web link" help="This can be copied from the dataset-download-button"/>
190 <param name="blobplot_cont_curated" type="data" format="png" label="Select blobplot contamination plot file"/>
191
192 <conditional name="hap2_curated_data">
193 <param name="hap2_exists_curated" type="select" label="Do you have data for Hap2?">
194 <option value="no" selected="true">No</option>
195 <option value="yes">Yes</option>
196 </param>
197 <when value="no"/>
198 <when value="yes">
199 <param name="gfstats_nstar_report_hap2_curated" type="data" format="txt" label="Select curated gfastats--nstar report file for hap2"/>
200 <param name="busco_short_summary_hap2_curated" type="data" format="txt" label="Select curated busco_short_summary.txt file for hap2"/>
201 <param name="mercury_qv_hap2_curated" type="data" format="txt" label="Select curated Merqury results .qv file for hap2"/>
202 <param name="merqury_completeness_stats_hap2_curated" type="data" format="txt" label="Select curated Merqury results completeness.stats file for hap2"/>
203 <param name="merqury_hap_spectra_cn_hap2_curated" type="data" format="png" label="Select Merqury results HAP1 spectra-cn.ln.png file for hap2"/>
204 <param name="merqury_spectra_cn_hap2_curated" type="data" format="png" label="Select Merqury HAP2 spectra-cn.ln.png file"/>
205 <param name="merqury_spectra_asm_hap2_curated" type="data" format="png" label="Select curated Merqury results spectra-asm.ln.png file for hap2"/>
206 <param name="hic_FullMap_hap2_curated" type="data" format="png" label="Select pretext FullMap plot for hap2"/>
207 <param name="hic_FullMap_link_hap2_curated" type="text" value="" label="Insert .pretext file web link for hap2" help="This can be copied from the dataset-download-button"/>
208 <param name="blobplot_cont_hap2_curated" type="data" format="png" label="Select blobplot contamination plot for hap2"/>
209 </when>
210 </conditional>
211 </section>
212
213 <!-- Input parameters for Curation notes -->
214 <section name="curation_notes" title="Curation Notes">
215 <param name="obs_haploid_num" type="text" optional="False" label="Insert observed haploid number"/>
216 <param name="obs_sex" type="select" label="Select observed sex" help="Example: XX, XY, X0, ZZ, ZW, NA">
217 <option value="XX">XX</option>
218 <option value="XY">XY</option>
219 <option value="X0">X0</option>
220 <option value="ZZ">ZZ</option>
221 <option value="ZW">ZW</option>
222 <option value="NA">NA</option>
223 </param>
224 <param name="interventions_per_gb" type="text" label="Insert manual intervention during curation (GB)"/>
225 <param name="contam_notes" type="text" label="Insert contamination notes"/>
226 <param name="other_notes" type="text" label="Insert Other notes"/>
227 </section>
228 </inputs>
229
230 <outputs>
231 <data name="EAR_pdf" format="pdf" from_work_dir="EAR.pdf" label="${tool.name} on ${on_string}: Output PDF" ></data>
232 <data name="log" format="txt" from_work_dir="EAR.log" label="${tool.name} on ${on_string}: Log file"/>
233 </outputs>
234 <tests>
235 <test expect_num_outputs="2">
236 <section name="sample_information">
237 <param name="tolid" value="xgPhyFlav1"/>
238 <param name="species_name" value="Phyllidia flava"/>
239 <param name="species_sex" value="XX"/>
240 <param name="submitter" value="John Doe"/>
241 <param name="affiliation" value="Galaxy EU"/>
242 <param name="tags" value="ERGA-BGE"/>
243 </section>
244 <section name="sequencing_data">
245 <repeat name="seq_data_info">
246 <param name="seq_data" value="HiFi: 40x"/>
247 </repeat>
248 <repeat name="seq_data_info">
249 <param name="seq_data" value="Bionano: 10x"/>
250 </repeat>
251 <repeat name="seq_data_info">
252 <param name="seq_data" value="OmniC: 90x"/>
253 </repeat>
254 </section>
255 <section name="genome_profiling_data">
256 <param name="genome_scope_summary" value="genomescope_results_summary.txt"/>
257 <param name="smudge_plot_summary" value="smudgeplot_verbose_summary.txt"/>
258 </section>
259 <section name="pre_curation_assembly_data">
260 <param name="haplotype_selection" value="hap1"/>
261 <param name="gfstats_nstar_report_precuration" value="ele_pre.asm1_gfastats.txt"/>
262 <param name="busco_short_summary_precuration" value="short_summary.specific.mammalia_odb10.pre.asm1.txt"/>
263 <param name="mercury_qv_precuration" value="ele_pre_merqOutput.qv"/>
264 <param name="merqury_completeness_stats_precuration" value="ele_pre_merqOutput.completeness.stats"/>
265 <conditional name="hap2_precuration_data">
266 <param name="hap2_exists_precuration" value="yes"/>
267 <param name="gfstats_nstar_report_hap2_precuration" value="ele_pre.asm2_gfastats.txt"/>
268 <param name="busco_short_summary_hap2_precuration" value="short_summary.specific.mammalia_odb10.pre.asm2.txt"/>
269 <param name="mercury_qv_hap2_precuration" value="ele_pre_merqOutput.qv"/>
270 <param name="merqury_completeness_stats_hap2_precuration" value="ele_pre_merqOutput.completeness.stats"/>
271 </conditional>
272 </section>
273 <section name="curated_assembly_data">
274 <param name="gfstats_nstar_report_curated" value="ele.asm1_post_gfastats.txt"/>
275 <param name="busco_short_summary_curated" value="short_summary.specific.mammalia_odb10.post.asm1.txt"/>
276 <param name="mercury_qv_curated" value="ele_post_merqOutput.qv"/>
277 <param name="merqury_completeness_stats_curated" value="ele_post_merqOutput.completeness.stats"/>
278 <param name="merqury_hap_spectra_cn_curated" value="ele_post_merqOutput.ele_post.asm1.spectra-cn.ln.png"/>
279 <param name="merqury_spectra_cn_curated" value="ele_post_merqOutput.spectra-cn.ln.png"/>
280 <param name="merqury_spectra_asm_curated" value="ele_post_merqOutput.spectra-asm.ln.png"/>
281 <param name="hic_FullMap_curated" value="pretext_snake1.png"/>
282 <param name="hic_FullMap_link_curated" value="https://box.fu-berlin.de/apps/files/something"/>
283 <param name="blobplot_cont_curated" value="blob1.png"/>
284 <conditional name="hap2_curated_data">
285 <param name="hap2_exists_curated" value="yes"/>
286 <param name="gfstats_nstar_report_hap2_curated" value="ele.asm2_post_gfastats.txt"/>
287 <param name="busco_short_summary_hap2_curated" value="short_summary.specific.mammalia_odb10.post.asm2.txt"/>
288 <param name="mercury_qv_hap2_curated" value="ele_post_merqOutput.qv"/>
289 <param name="merqury_completeness_stats_hap2_curated" value="ele_post_merqOutput.completeness.stats"/>
290 <param name="merqury_hap_spectra_cn_hap2_curated" value="ele_post_merqOutput.ele_post.asm2.spectra-cn.ln.png"/>
291 <param name="merqury_spectra_cn_hap2_curated" value="ele_post_merqOutput.spectra-cn.ln.png"/>
292 <param name="merqury_spectra_asm_hap2_curated" value="ele_post_merqOutput.spectra-asm.ln.png"/>
293 <param name="hic_FullMap_hap2_curated" value="pretext_snake2.png"/>
294 <param name="hic_FullMap_link_hap2_curated" value="https://box.fu-berlin.de/apps/files/something"/>
295 <param name="blobplot_cont_hap2_curated" value="blob2.png"/>
296 </conditional>
297 </section>
298 <section name="curation_notes">
299 <param name="obs_haploid_num" value="28"/>
300 <param name="obs_sex" value="XX"/>
301 <param name="interventions_per_gb" value="2"/>
302 <param name="contam_notes" value="No presence of contaminants. Mitochondrial genome was removed from the assembly"/>
303 <param name="other_notes" value="Large collapsed repeat in chr5, haplotypic inversion in chr12"/>
304 </section>
305 <output name="EAR_pdf" file="EAR.pdf" ftype="pdf" compare="sim_size"/>
306 <output name="log" file="EAR_log"/>
307 </test>
308 </tests>
309 <help><![CDATA[
310
311 .. class:: infomark
312
313 **What it does**
314
315 **ERGA Assembly Reporting Tool (EAR)** is a tool that compiles various statistics and reports generated from Assembly pipeline tools and compiles them in to a summarized PDF document for reporting.
316 ]]></help>
317 <expand macro="citations"/>
318 <expand macro="creator"/>
319 </tool>