Mercurial > repos > artbio > sr_bowtie
comparison sRbowtie.xml @ 8:8157d59a8190 draft default tip
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 269546398f6e244a5df4aa2108bb4705fad15f7a
| author | artbio |
|---|---|
| date | Thu, 07 Nov 2024 15:58:27 +0000 |
| parents | 3d5bd42097d7 |
| children |
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| 7:3d5bd42097d7 | 8:8157d59a8190 |
|---|---|
| 1 <tool id="bowtieForSmallRNA" name="sR_bowtie" version="2.3.0"> | 1 <tool id="bowtieForSmallRNA" name="sR_bowtie" version="2.3.1"> |
| 2 <description>for small RNA short reads</description> | 2 <description>for small RNA short reads</description> |
| 3 <xrefs> | |
| 4 <xref type="bio.tools">sr_bowtie</xref> | |
| 5 </xrefs> | |
| 3 <requirements> | 6 <requirements> |
| 4 <requirement type="package" version="1.3.1">bowtie</requirement> | 7 <requirement type="package" version="1.3.1">bowtie</requirement> |
| 5 <requirement type="package" version="1.14">samtools</requirement> | 8 <requirement type="package" version="1.14">samtools</requirement> |
| 6 </requirements> | 9 </requirements> |
| 7 <command detect_errors="exit_code"><![CDATA[ | 10 <command detect_errors="exit_code"><![CDATA[ |
| 130 <data format_source="input" label="Unmatched reads" name="unaligned"> | 133 <data format_source="input" label="Unmatched reads" name="unaligned"> |
| 131 <filter>additional_fasta == "unal" or additional_fasta == "al_and_unal"</filter> | 134 <filter>additional_fasta == "unal" or additional_fasta == "al_and_unal"</filter> |
| 132 </data> | 135 </data> |
| 133 </outputs> | 136 </outputs> |
| 134 <tests> | 137 <tests> |
| 135 <test> | 138 <test expect_num_outputs="1"> |
| 136 <param name="genomeSource" value="history" /> | 139 <param name="genomeSource" value="history" /> |
| 137 <param ftype="fasta" name="ownFile" value="297_reference.fa" /> | 140 <param ftype="fasta" name="ownFile" value="297_reference.fa" /> |
| 138 <param name="method" value="unique" /> | 141 <param name="method" value="unique" /> |
| 139 <param ftype="fasta" name="input" value="input.fa" /> | 142 <param ftype="fasta" name="input" value="input.fa" /> |
| 140 <param name="v_mismatches" value="1" /> | 143 <param name="v_mismatches" value="1" /> |
| 141 <param name="output_format" value="bam" /> | 144 <param name="output_format" value="bam" /> |
| 142 <output file="output.bam" ftype="bam" compare="sim_size" delta="1000" name="output" /> | 145 <output file="output.bam" ftype="bam" compare="sim_size" delta="1000" name="output" /> |
| 143 </test> | 146 </test> |
| 144 <test> | 147 <test expect_num_outputs="1"> |
| 145 <param name="genomeSource" value="history" /> | 148 <param name="genomeSource" value="history" /> |
| 146 <param ftype="fasta" name="ownFile" value="297_reference.fa" /> | 149 <param ftype="fasta" name="ownFile" value="297_reference.fa" /> |
| 147 <param name="method" value="unique" /> | 150 <param name="method" value="unique" /> |
| 148 <param ftype="fastq" name="input" value="input.fastq" /> | 151 <param ftype="fastq" name="input" value="input.fastq" /> |
| 149 <param name="v_mismatches" value="1" /> | 152 <param name="v_mismatches" value="1" /> |
| 150 <param name="output_format" value="bam" /> | 153 <param name="output_format" value="bam" /> |
| 151 <output file="output2.bam" ftype="bam" compare="sim_size" delta="1000" name="output" /> | 154 <output file="output2.bam" ftype="bam" compare="sim_size" delta="1000" name="output" /> |
| 152 </test> | 155 </test> |
| 153 <test> | 156 <test expect_num_outputs="2"> |
| 154 <param name="genomeSource" value="history" /> | 157 <param name="genomeSource" value="history" /> |
| 155 <param ftype="fasta" name="ownFile" value="297_reference.fa" /> | 158 <param ftype="fasta" name="ownFile" value="297_reference.fa" /> |
| 156 <param name="method" value="unique" /> | 159 <param name="method" value="unique" /> |
| 157 <param ftype="fastqsanger" name="input" value="input.fastqsanger" /> | 160 <param ftype="fastqsanger" name="input" value="input.fastqsanger" /> |
| 158 <param name="v_mismatches" value="1" /> | 161 <param name="v_mismatches" value="1" /> |
| 159 <param name="additional_fasta" value="al" /> | 162 <param name="additional_fasta" value="al" /> |
| 160 <param name="output_format" value="bam" /> | 163 <param name="output_format" value="bam" /> |
| 161 <output file="output2.bam" ftype="bam" compare="sim_size" delta="1000" name="output" /> | 164 <output file="output2.bam" ftype="bam" compare="sim_size" delta="1000" name="output" /> |
| 162 <output file="al.fastqsanger" ftype="fastqsanger" name="aligned" /> | 165 <output file="al.fastqsanger" ftype="fastqsanger" name="aligned" /> |
| 163 </test> | 166 </test> |
| 164 <test> | 167 <test expect_num_outputs="1"> |
| 165 <param name="genomeSource" value="history" /> | 168 <param name="genomeSource" value="history" /> |
| 166 <param ftype="fasta" name="ownFile" value="297_reference.fa" /> | 169 <param ftype="fasta" name="ownFile" value="297_reference.fa" /> |
| 167 <param name="method" value="multiple" /> | 170 <param name="method" value="multiple" /> |
| 168 <param ftype="fasta" name="input" value="input.fa" /> | 171 <param ftype="fasta" name="input" value="input.fa" /> |
| 169 <param name="v_mismatches" value="1" /> | 172 <param name="v_mismatches" value="1" /> |
| 170 <param name="output_format" value="tabular" /> | 173 <param name="output_format" value="tabular" /> |
| 171 <output file="output.tab" ftype="tabular" name="output" /> | 174 <output file="output.tab" ftype="tabular" name="output" /> |
| 172 </test> | 175 </test> |
| 173 <test> | 176 <test expect_num_outputs="2"> |
| 174 <param name="genomeSource" value="history" /> | 177 <param name="genomeSource" value="history" /> |
| 175 <param ftype="fasta" name="ownFile" value="297_reference.fa" /> | 178 <param ftype="fasta" name="ownFile" value="297_reference.fa" /> |
| 176 <param name="method" value="multiple" /> | 179 <param name="method" value="multiple" /> |
| 177 <param ftype="fasta" name="input" value="input.fa" /> | 180 <param ftype="fasta" name="input" value="input.fa" /> |
| 178 <param name="v_mismatches" value="1" /> | 181 <param name="v_mismatches" value="1" /> |