Mercurial > repos > ieguinoa > ena_webin_cli

comparison ena_consensus_submit.xml @ 0:e25357392813 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author ieguinoa
date Tue, 18 May 2021 16:30:52 +0000
parents
children f24eb2f2cb0c
comparison
equal deleted inserted replaced
-1:000000000000 0:e25357392813
1 <tool id="ena_consensus_submit" name="Submit consensus sequence to ENA" version="0.1.0" python_template_version="3.5">
2 <macros>
3 <token name="@VERSION@">3.7.0</token>
4 </macros>
5 <requirements>
6 <requirement type="package" version="@VERSION@">ena-webin-cli</requirement>
7 <requirement type="package" version="1.76">biopython</requirement>
8 <requirement type="package" version="5.3">pyyaml</requirement>
9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[
11
12 webin_id=`grep 'username' $credentials | cut -f2,2`;
13 if [ "\$webin_id" = "" ]; then
14 ## No credentials in user defined preferences
15 ## Fallback to global defined credentials (if exist)
16 #import os
17 #if os.path.isfile(os.environ.get('GALAXY_ENA_SECRETS', '')):
18 credentials_path=\${GALAXY_ENA_SECRETS};
19 webin_id=`grep 'username' \$GALAXY_ENA_SECRETS | cut -d' ' -f2,2`;
20 password=`grep 'password' \$GALAXY_ENA_SECRETS | cut -d' ' -f2,2`;
21 if [ "\$webin_id" = "" ]; then
22 echo "No global credentials defined. Check your GALAXY_ENA_SECRETS file or set your credentials via: User -> Preferences -> Manage Information";
23 exit 1;
24 fi;
25 #else:
26 echo "No ENA credentials defined. Set your credentials via: User -> Preferences -> Manage Information";
27 exit 1;
28 #end if
29 else
30 password=`grep 'password' $credentials | cut -f2,2`;
31 fi;
32
33 ## if it is still running at this point then the webin_id and password are set
34
35 ## create a manifaste base file with the parameters that are identical for all sequences that will be submited (if submitting a multifasta)
36 #set $manifest_base = 'manifest_base.tab'
37 mkdir manifests;
38 mkdir fasta;
39
40 echo -e "ASSEMBLY_TYPE\t$assembly_type" >> $manifest_base;
41 echo -e "COVERAGE\t$coverage" >> $manifest_base;
42 echo -e "PROGRAM\t$assembly_program" >> $manifest_base;
43 echo -e "MINGAPLENGTH\t$min_gap_length" >> $manifest_base;
44 echo -e "MOLECULETYPE\t$molecule_type" >> $manifest_base;
45
46 #if $metadata_file_or_form.metadata_format == "file":
47 ## process the input tables, this creates an intermediate file with information
48 python3 '$__tool_directory__/process_input.py' $metadata_file_or_form.ena_receipt $genome_fasta './manifests' './fasta' $manifest_base;
49 center_name=`grep 'center_name' $metadata_file_or_form.ena_receipt | cut -f2,2 | tr -d '\n'`;
50 #else:
51 #set $generated_manifest='./manifests/generated_manifest.txt'
52 cp $manifest_base $generated_manifest
53 $study_id = $metadata_file_or_form.study_accession
54 $sample_id = $metadata_file_or_form.sample_accession
55 echo "STUDY\t$study_id" > $generated_manifest;
56 echo "SAMPLE\t$sample_id" >> $generated_manifest;
57 center_name=$metadata_file_or_form.center_name;
58 echo "ASSEMBLY_NAME\t$metadata_file_or_form.assembly_name" >> $generated_manifest;
59 echo "PLATFORM\t$platform_name" >> $generated_manifest;
60 #end if
61
62
63 #if $metadata_file_or_form.metadata_format == "file":
64 ## iterate over the list of manifest - fasta generated by the process_input
65 ## in case of errors, this list is empty
66 while read line; do
67 manifest=`echo \$line | cut -d' ' -f1,1`;
68 ena-webin-cli
69 -context genome
70 -userName \$webin_id
71 -password \$password
72 -centerName \$center_name
73 -manifest \$manifest
74 -inputDir "./fasta"
75 #if $dry_run == "true":
76 -validate
77 #end if
78 ;
79 done < submit_list.tab
80
81 #else:
82 gzip -c $genome_fasta > consensus.fasta.gz;
83 echo -e "FASTA\tconsensus.fasta.gz" >> $generated_manifest;
84 ena-webin-cli
85 -context genome
86 -userName \$webin_id
87 -password \$password
88 -centerName '\$center_name'
89 -manifest $generated_manifest
90 -inputDir "./"
91 #if $submit_test == "true":
92 -test
93 #end if
94 #if $dry_run == "true":
95 -validate
96 #else:
97 -submit
98 #end if
99 #end if
100 ]]></command>
101 <configfiles>
102 <configfile name="credentials"><![CDATA[
103 #set $webin_id = $__user__.extra_preferences.get('ena_webin_account|webin_id', "").strip()
104 #set $password = $__user__.extra_preferences.get('ena_webin_account|password', "").strip()
105 #if $webin_id != "":
106 username\t"$webin_id"
107 password\t"$password"
108 #end if
109 ]]></configfile>
110 </configfiles>
111 <inputs>
112 <param name="submit_test" type="boolean" default="False" label="Submit to test server" help="Suggested to test metadata format" />
113 <param name="dry_run" type="boolean" default="False" label="Validate files and metadata but do not submit" help="Generate input files and run Webin-CLI with -validate option."/>
114 <param name="genome_fasta" type="data" label="Select the consensus sequence assembly file" format="fasta"/>
115 <param name="assembly_type" type="select" label="Assembly type">
116 <option value="clone">Clone</option>
117 <option value="isolate">Isolate</option>
118 </param>
119 <param name="assembly_program" type="text" optional="False" label="Assembly program"/>
120 <param name="molecule_type" type="select" label="Molecule type">
121 <option value="genomic RNA" selected="True">genomic RNA</option>
122 <option value="viral cRNA">viral cRNA</option>
123 <option value="genomic DNA">genomic DNA</option>
124 </param>
125 <param name="min_gap_length" type="text" optional="True" label="Minimum gap length"/>
126 <param name="coverage" type="float" optional="False" value="10000" label="Coverage"/>
127 <conditional name="metadata_file_or_form">
128 <param name="metadata_format" type="select" label="Select the method to load study and sample metadata">
129 <option value="file" selected="True">I used Galaxy ENA upload tool for raw data submission, parse my submission receipt</option>
130 <option value="form">Fill in required metadata for linking</option>
131 </param>
132 <when value="file">
133 <param type="data" format="txt" name="ena_receipt" label="Submission receipt obtained from ENA upload tool"/>
134 </when>
135 <when value="form">
136 <param name="assembly_name" type="text" optional="False" label="Assembly name"/>
137 <param name="study_accession" type="text" optional="False" label="Study accession or unique name (alias)"/>
138 <param name="sample_accession" type="text" optional="False" label="Sample accession or unique name (alias)"/>
139 <param name="sequencing_platform" type="text" optional="False" label="Sequencing platform"/>
140 <param name="description" type="text" optional="True" value="" label="Description" help="Free text description of the genome assembly (optional)"/>
141 <param name="center_name" type="text" optional="False" label="Center name"/>
142 </when>
143 </conditional>
144 </inputs>
145 <outputs>
146 <collection name="generated_manifests" type="list" label="Generated manifests">
147 <!--<discover_datasets pattern="__name_and_ext__" directory="manifests" />-->
148 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.manifest\.txt$" ext="txt" directory="manifests" />
149 </collection>
150 <collection name="manifests_reports" type="list" label="Manifests reports">
151 <!--[><discover_datasets pattern="__name_and_ext__" directory="manifests" /><]-->
152 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.manifest\.txt\.report$" ext="txt" directory="manifests" />
153 </collection>
154 <data name="webin_cli_report" label="ENA submission receipt" format="txt" from_work_dir="manifests/webin-cli.report"/>
155 </outputs>
156 <help><![CDATA[
157 TODO: Fill in help.
158 ]]></help>
159 </tool>