Mercurial > repos > artbio > repenrich2
comparison repenrich2.xml @ 5:08e50af788f7 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit b1761de76fd068b86a06d88e70c1ba1d8644e7b5
| author | artbio |
|---|---|
| date | Sun, 21 Apr 2024 21:52:40 +0000 |
| parents | c5bb2f9af708 |
| children | 388a47ca4199 |
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| 4:c5bb2f9af708 | 5:08e50af788f7 |
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| 100 | 100 |
| 101 <param format="txt" label="RepeatMasker description file" name="repeatmasker" type="data" help="see help section"/> | 101 <param format="txt" label="RepeatMasker description file" name="repeatmasker" type="data" help="see help section"/> |
| 102 </inputs> | 102 </inputs> |
| 103 | 103 |
| 104 <outputs> | 104 <outputs> |
| 105 <data format="tabular" name="unique_mapper_counts" label="RepEnrich on ${on_string}: unique mapper counts" from_work_dir="unique_mapper_counts.tsv" /> | |
| 105 <data format="tabular" name="class_fraction_counts" label="RepEnrich on ${on_string}: class fraction counts" from_work_dir="class_fraction_counts.tsv" /> | 106 <data format="tabular" name="class_fraction_counts" label="RepEnrich on ${on_string}: class fraction counts" from_work_dir="class_fraction_counts.tsv" /> |
| 106 <data format="tabular" name="family_fraction_counts" label="RepEnrich on ${on_string}: family fraction counts" from_work_dir="family_fraction_counts.tsv" /> | 107 <data format="tabular" name="family_fraction_counts" label="RepEnrich on ${on_string}: family fraction counts" from_work_dir="family_fraction_counts.tsv" /> |
| 107 <data format="tabular" name="fraction_counts" label="RepEnrich on ${on_string}: fraction counts" from_work_dir="fraction_counts.tsv" /> | 108 <data format="tabular" name="fraction_counts" label="RepEnrich on ${on_string}: fraction counts" from_work_dir="fraction_counts.tsv" /> |
| 108 </outputs> | 109 </outputs> |
| 109 | 110 |
| 112 <param name="seq_method_list" value="single-read"/> | 113 <param name="seq_method_list" value="single-read"/> |
| 113 <param name="input_fastq" value="chrY-500k.R1.fastqsanger.gz" ftype="fastq.gz"/> | 114 <param name="input_fastq" value="chrY-500k.R1.fastqsanger.gz" ftype="fastq.gz"/> |
| 114 <param name="genomeSource" value="history"/> | 115 <param name="genomeSource" value="history"/> |
| 115 <param name="genome" value="chrY-1-500k.fa" ftype="fasta"/> | 116 <param name="genome" value="chrY-1-500k.fa" ftype="fasta"/> |
| 116 <param name="repeatmasker" value="chrY-1-500k.fa.out" ftype="txt"/> | 117 <param name="repeatmasker" value="chrY-1-500k.fa.out" ftype="txt"/> |
| 118 <output name="unique_mapper_counts" file="chrY_single_unique_mapper_counts.tab" ftype="tabular"/> | |
| 117 <output name="class_fraction_counts" file="chrY_single_class_fraction_counts.tab" ftype="tabular"/> | 119 <output name="class_fraction_counts" file="chrY_single_class_fraction_counts.tab" ftype="tabular"/> |
| 118 <output name="family_fraction_counts" file="chrY_single_family_fraction_counts.tab" ftype="tabular"/> | 120 <output name="family_fraction_counts" file="chrY_single_family_fraction_counts.tab" ftype="tabular"/> |
| 119 <output name="fraction_counts" file="chrY_single_fraction_counts.tab" ftype="tabular"/> | 121 <output name="fraction_counts" file="chrY_single_fraction_counts.tab" ftype="tabular"/> |
| 120 </test> | 122 </test> |
| 121 <test> | 123 <test> |
| 123 <param name="input_fastq" value="chrY-500k.R1.fastqsanger.gz" ftype="fastq.gz"/> | 125 <param name="input_fastq" value="chrY-500k.R1.fastqsanger.gz" ftype="fastq.gz"/> |
| 124 <param name="input2_fastq" value="chrY-500k.R2.fastqsanger.gz" ftype="fastq.gz"/> | 126 <param name="input2_fastq" value="chrY-500k.R2.fastqsanger.gz" ftype="fastq.gz"/> |
| 125 <param name="genomeSource" value="history"/> | 127 <param name="genomeSource" value="history"/> |
| 126 <param name="genome" value="chrY-1-500k.fa" ftype="fasta"/> | 128 <param name="genome" value="chrY-1-500k.fa" ftype="fasta"/> |
| 127 <param name="repeatmasker" value="chrY-1-500k.fa.out" ftype="txt"/> | 129 <param name="repeatmasker" value="chrY-1-500k.fa.out" ftype="txt"/> |
| 130 <output name="unique_mapper_counts" file="chrY_paired_unique_mapper_counts.tab" ftype="tabular"/> | |
| 128 <output name="class_fraction_counts" file="chrY_paired_class_fraction_counts.tab" ftype="tabular"/> | 131 <output name="class_fraction_counts" file="chrY_paired_class_fraction_counts.tab" ftype="tabular"/> |
| 129 <output name="family_fraction_counts" file="chrY_paired_family_fraction_counts.tab" ftype="tabular"/> | 132 <output name="family_fraction_counts" file="chrY_paired_family_fraction_counts.tab" ftype="tabular"/> |
| 130 <output name="fraction_counts" file="chrY_paired_fraction_counts.tab" ftype="tabular"/> | 133 <output name="fraction_counts" file="chrY_paired_fraction_counts.tab" ftype="tabular"/> |
| 131 </test> | 134 </test> |
| 132 </tests> | 135 </tests> |