Mercurial > repos > kkonganti > cfsan_cronology

comparison cfsan_cronology.xml @ 13:1e6a6e88db16

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planemo upload
author kkonganti
date Mon, 15 Jul 2024 16:26:46 -0400
parents 78a02e8cb092
children
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12:78a02e8cb092 13:1e6a6e88db16
4 <container type="docker">quay.io/biocontainers/nextflow:24.04.3--hdfd78af_0</container> 4 <container type="docker">quay.io/biocontainers/nextflow:24.04.3--hdfd78af_0</container>
5 </requirements> 5 </requirements>
6 <version_command>nextflow -version</version_command> 6 <version_command>nextflow -version</version_command>
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 mkdir -p cpipes-input || exit 1; 8 mkdir -p cpipes-input || exit 1;
9 echo -e 'We attempted to create a tree and upload to microreact.org. The following is the log of that attempt\\nand contains the URL if it was successful.\\n\\n' > upload_to_microreact.txt || exit 1; 9 echo -e 'We attempted to create a tree and upload to microreact.org. The following is the log of that attempt\nand contains the URL if it was successful.\n\n' > upload_to_microreact.txt || exit 1;
10 pwd_path=\$(pwd); 10 pwd_path=\$(pwd);
11 #import re 11 #import re
12 #if (str($input_read_type_cond.input_read_type) == "single_long"): 12 #if (str($input_read_type_cond.input_read_type) == "single_long"):
13 #for _, $unpaired in enumerate($input_read_type_cond.input): 13 #for _, $unpaired in enumerate($input_read_type_cond.input):
14 #set read1 = str($unpaired.name) 14 #set read1 = str($unpaired.name)
32 #end if 32 #end if
33 ln -sf '$pair.forward' './cpipes-input/$read_R1'; 33 ln -sf '$pair.forward' './cpipes-input/$read_R1';
34 ln -sf '$pair.reverse' './cpipes-input/$read_R2'; 34 ln -sf '$pair.reverse' './cpipes-input/$read_R2';
35 #end for 35 #end for
36 #end if 36 #end if
37 $__tool_directory__/0.1.0/cpipes 37 $__tool_directory__/0.2.0/cpipes
38 --pipeline cronology 38 --pipeline cronology
39 --input \${pwd_path}/cpipes-input 39 --input \${pwd_path}/cpipes-input
40 --output \${pwd_path}/cpipes-output 40 --output \${pwd_path}/cpipes-output
41 --fq_suffix '${input_read_type_cond.fq_suffix}' 41 --fq_suffix '${input_read_type_cond.fq_suffix}'
42 #if (str($input_read_type_cond.input_read_type) == "single_long"): 42 #if (str($input_read_type_cond.input_read_type) == "single_long"):
48 --tuspy_n $tuspy_n 48 --tuspy_n $tuspy_n
49 --fq_filename_delim '${fq_filename_delim}' 49 --fq_filename_delim '${fq_filename_delim}'
50 --fq_filename_delim_idx $fq_filename_delim_idx 50 --fq_filename_delim_idx $fq_filename_delim_idx
51 -profile gxkubernetes; 51 -profile gxkubernetes;
52 mv './cpipes-output/cronology-multiqc/multiqc_report.html' './multiqc_report.html' || exit 1; 52 mv './cpipes-output/cronology-multiqc/multiqc_report.html' './multiqc_report.html' || exit 1;
53 mv './cpipes-output/mashtree/hitsTree.dnd' './hitsTree.newick' > || exit 1; 53 mv './cpipes-output/mashtree/hitsTree.dnd' './hitsTree.newick' || exit 1;
54 cat ./cpipes-output/upload_microreact/microreact_url.txt >> upload_to_microreact.txt || exit 1; 54 cat ./cpipes-output/upload_microreact/microreact_url.txt >> upload_to_microreact.txt || exit 1;
55 ]]></command> 55 ]]></command>
56 <inputs> 56 <inputs>
57 <conditional name="input_read_type_cond"> 57 <conditional name="input_read_type_cond">
58 <param name="input_read_type" type="select" label="Select the read collection type"> 58 <param name="input_read_type" type="select" label="Select the read collection type">