Mercurial > repos > devteam > fastqc
comparison rgFastQC.xml @ 16:ff9530579d1f draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 9a987a679243f52297c465180da0bb557a3d0fa7
| author | iuc |
|---|---|
| date | Sun, 14 Jan 2018 09:31:51 -0500 |
| parents | 2b0c9d9fc6ca |
| children | c15237684a01 |
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| 15:2b0c9d9fc6ca | 16:ff9530579d1f |
|---|---|
| 1 <tool id="fastqc" name="FastQC" version="0.70"> | 1 <tool id="fastqc" name="FastQC" version="0.71"> |
| 2 <description>Read Quality reports</description> | 2 <description>Read Quality reports</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="package" version="0.11.5">fastqc</requirement> | 4 <requirement type="package" version="0.11.6">fastqc</requirement> |
| 5 </requirements> | 5 </requirements> |
| 6 <command detect_errors="exit_code"><![CDATA[ | 6 <command detect_errors="exit_code"><![CDATA[ |
| 7 #import re | 7 #import re |
| 8 #set input_name = re.sub('[^\w\-\s]', '_', str($input_file.element_identifier)) | 8 #set input_name = re.sub('[^\w\-\s]', '_', str($input_file.element_identifier)) |
| 9 | 9 |
| 20 #elif 'sam' in $input_file.ext: | 20 #elif 'sam' in $input_file.ext: |
| 21 #set format = 'sam' | 21 #set format = 'sam' |
| 22 #else | 22 #else |
| 23 #set format = 'fastq' | 23 #set format = 'fastq' |
| 24 #end if | 24 #end if |
| 25 | |
| 26 | 25 |
| 27 ln -s '${input_file}' '${input_file_sl}' && | 26 ln -s '${input_file}' '${input_file_sl}' && |
| 28 mkdir -p '${html_file.files_path}' && | 27 mkdir -p '${html_file.files_path}' && |
| 29 fastqc | 28 fastqc |
| 30 --outdir '${html_file.files_path}' | 29 --outdir '${html_file.files_path}' |
| 61 <tests> | 60 <tests> |
| 62 <test> | 61 <test> |
| 63 <param name="input_file" value="1000gsample.fastq" /> | 62 <param name="input_file" value="1000gsample.fastq" /> |
| 64 <param name="contaminants" value="fastqc_contaminants.txt" ftype="tabular" /> | 63 <param name="contaminants" value="fastqc_contaminants.txt" ftype="tabular" /> |
| 65 <output name="html_file" file="fastqc_report.html" ftype="html" lines_diff="100"/> | 64 <output name="html_file" file="fastqc_report.html" ftype="html" lines_diff="100"/> |
| 66 <output name="text_file" file="fastqc_data.txt" ftype="txt" lines_diff="2"/> | 65 <output name="text_file" file="fastqc_data.txt" ftype="txt" lines_diff="4"/> |
| 67 </test> | 66 </test> |
| 68 <test> | 67 <test> |
| 69 <param name="input_file" value="1000gsample.fastq" /> | 68 <param name="input_file" value="1000gsample.fastq" /> |
| 70 <param name="limits" value="fastqc_customlimits.txt" ftype="txt" /> | 69 <param name="limits" value="fastqc_customlimits.txt" ftype="txt" /> |
| 71 <output name="html_file" file="fastqc_report2.html" ftype="html" compare="sim_size" delta="4096"/> | 70 <output name="html_file" file="fastqc_report2.html" ftype="html" compare="sim_size" delta="4096"/> |
| 72 <output name="text_file" file="fastqc_data2.txt" ftype="txt" lines_diff="2"/> | 71 <output name="text_file" file="fastqc_data2.txt" ftype="txt" lines_diff="4"/> |
| 73 </test> | 72 </test> |
| 74 <test> | 73 <test> |
| 75 <param name="input_file" value="1000gsample.fastq.gz" ftype="fastq.gz" /> | 74 <param name="input_file" value="1000gsample.fastq.gz" ftype="fastq.gz" /> |
| 76 <param name="contaminants" value="fastqc_contaminants.txt" ftype="tabular" /> | 75 <param name="contaminants" value="fastqc_contaminants.txt" ftype="tabular" /> |
| 77 <output name="html_file" file="fastqc_report.html" ftype="html" lines_diff="100"/> | 76 <output name="html_file" file="fastqc_report.html" ftype="html" lines_diff="100"/> |
| 78 <output name="text_file" file="fastqc_data.txt" ftype="txt" lines_diff="2"/> | 77 <output name="text_file" file="fastqc_data.txt" ftype="txt" lines_diff="4"/> |
| 79 </test> | 78 </test> |
| 80 <test> | 79 <test> |
| 81 <param name="input_file" value="1000gsample.fastq.bz2" ftype="fastq.bz2" /> | 80 <param name="input_file" value="1000gsample.fastq.bz2" ftype="fastq.bz2" /> |
| 82 <param name="contaminants" value="fastqc_contaminants.txt" ftype="tabular" /> | 81 <param name="contaminants" value="fastqc_contaminants.txt" ftype="tabular" /> |
| 83 <output name="html_file" file="fastqc_report.html" ftype="html" lines_diff="100"/> | 82 <output name="html_file" file="fastqc_report.html" ftype="html" lines_diff="100"/> |
| 84 <output name="text_file" file="fastqc_data.txt" ftype="txt" lines_diff="2"/> | 83 <output name="text_file" file="fastqc_data.txt" ftype="txt" lines_diff="4"/> |
| 85 </test> | 84 </test> |
| 86 <test> | 85 <test> |
| 87 <param name="input_file" value="hisat_output_1.bam" ftype="bam" /> | 86 <param name="input_file" value="hisat_output_1.bam" ftype="bam" /> |
| 88 <output name="html_file" file="fastqc_report_hisat.html" ftype="html" lines_diff="100"/> | 87 <output name="html_file" file="fastqc_report_hisat.html" ftype="html" lines_diff="100"/> |
| 89 <output name="text_file" file="fastqc_data_hisat.txt" ftype="txt" lines_diff="2"/> | 88 <output name="text_file" file="fastqc_data_hisat.txt" ftype="txt" lines_diff="4"/> |
| 90 </test> | 89 </test> |
| 91 </tests> | 90 </tests> |
| 92 <help> | 91 <help> |
| 93 .. class:: infomark | 92 .. class:: infomark |
| 94 | 93 |