Mercurial > repos > peterjc > sample_seqs
comparison tools/sample_seqs/sample_seqs.xml @ 3:02c13ef1a669 draft
Uploaded v0.2.1, fixed missing test file, more tests.
| author | peterjc |
|---|---|
| date | Fri, 27 Mar 2015 09:34:27 -0400 |
| parents | da64f6a9e32b |
| children | d3aa9f25c24c |
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| 2:da64f6a9e32b | 3:02c13ef1a669 |
|---|---|
| 1 <tool id="sample_seqs" name="Sub-sample sequences files" version="0.2.0"> | 1 <tool id="sample_seqs" name="Sub-sample sequences files" version="0.2.1"> |
| 2 <description>e.g. to reduce coverage</description> | 2 <description>e.g. to reduce coverage</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="package" version="1.65">biopython</requirement> | 4 <requirement type="package" version="1.65">biopython</requirement> |
| 5 <requirement type="python-module">Bio</requirement> | 5 <requirement type="python-module">Bio</requirement> |
| 6 </requirements> | 6 </requirements> |
| 120 <test> | 120 <test> |
| 121 <param name="input_file" value="MID4_GLZRM4E04_rnd30_frclip.sff" ftype="sff" /> | 121 <param name="input_file" value="MID4_GLZRM4E04_rnd30_frclip.sff" ftype="sff" /> |
| 122 <param name="type" value="percentage" /> | 122 <param name="type" value="percentage" /> |
| 123 <param name="percent" value="20.0" /> | 123 <param name="percent" value="20.0" /> |
| 124 <output name="output_file" file="MID4_GLZRM4E04_rnd30_frclip.sample_N5.sff" ftype="sff"/> | 124 <output name="output_file" file="MID4_GLZRM4E04_rnd30_frclip.sample_N5.sff" ftype="sff"/> |
| 125 </test> | 125 <assert_stderr> |
| 126 <test> | 126 <has_line line="Sampling 20.000% of sequences" /> |
| 127 <param name="input_file" value="MID4_GLZRM4E04_rnd30_frclip.sff" ftype="sff" /> | 127 <has_line line="Selected 5 records" /> |
| 128 <param name="type" value="everyNth" /> | 128 </assert_stderr> |
| 129 <param name="percent" value="5" /> | 129 </test> |
| 130 <test> | |
| 131 <param name="input_file" value="MID4_GLZRM4E04_rnd30_frclip.sff" ftype="sff" /> | |
| 132 <param name="type" value="everyNth" /> | |
| 133 <param name="every_n" value="5" /> | |
| 130 <param name="interleaved" value="true" /> | 134 <param name="interleaved" value="true" /> |
| 131 <output name="output_file" file="MID4_GLZRM4E04_rnd30_frclip.pair_sample_N5.sff" ftype="sff"/> | 135 <output name="output_file" file="MID4_GLZRM4E04_rnd30_frclip.pair_sample_N5.sff" ftype="sff"/> |
| 132 </test> | 136 <assert_stderr> |
| 133 <test> | 137 <has_line line="Sampling every 5th sequence" /> |
| 134 <param name="input_file" value="MID4_GLZRM4E04_rnd30.sff" ftype="sff" /> | 138 <has_line line="Selected 3 pairs" /> |
| 135 <param name="type" value="desired_count" /> | 139 </assert_stderr> |
| 136 <param name="count" value="30" /> | 140 </test> |
| 137 <output name="output_file" file="MID4_GLZRM4E04_rnd30.sff" ftype="sff"/> | 141 <test> |
| 142 <param name="input_file" value="MID4_GLZRM4E04_rnd30_frclip.sff" ftype="sff" /> | |
| 143 <param name="type" value="desired_count" /> | |
| 144 <param name="count" value="25" /> | |
| 145 <output name="output_file" file="MID4_GLZRM4E04_rnd30_frclip.sff" ftype="sff"/> | |
| 146 <assert_stderr> | |
| 147 <has_line line="Input file has 25 sequences" /> | |
| 148 <has_line line="Taking all the sequences" /> | |
| 149 <has_line line="Selected 25 records" /> | |
| 150 </assert_stderr> | |
| 138 </test> | 151 </test> |
| 139 <test> | 152 <test> |
| 140 <param name="input_file" value="MID4_GLZRM4E04_rnd30_frclip.sff" ftype="sff" /> | 153 <param name="input_file" value="MID4_GLZRM4E04_rnd30_frclip.sff" ftype="sff" /> |
| 141 <param name="type" value="desired_count" /> | 154 <param name="type" value="desired_count" /> |
| 142 <param name="count" value="1" /> | 155 <param name="count" value="1" /> |
| 143 <output name="output_file" file="MID4_GLZRM4E04_rnd30_frclip.sample_C1.sff" ftype="sff"/> | 156 <output name="output_file" file="MID4_GLZRM4E04_rnd30_frclip.sample_C1.sff" ftype="sff"/> |
| 157 <assert_stderr> | |
| 158 <has_line line="Input file has 25 sequences" /> | |
| 159 <has_line line="Sampling just first sequence!" /> | |
| 160 <has_line line="Selected 1 records" /> | |
| 161 </assert_stderr> | |
| 162 </test> | |
| 163 <test expect_failure="true" expect_exit_code="1"> | |
| 164 <param name="input_file" value="MID4_GLZRM4E04_rnd30_frclip.sff" ftype="sff" /> | |
| 165 <param name="type" value="desired_count" /> | |
| 166 <param name="count" value="30" /> | |
| 167 <assert_stderr> | |
| 168 <has_line line="Input file has 25 sequences" /> | |
| 169 <has_line line="Requested 30 sequences, but file only has 25." /> | |
| 170 </assert_stderr> | |
| 144 </test> | 171 </test> |
| 145 </tests> | 172 </tests> |
| 146 <help> | 173 <help> |
| 147 **What it does** | 174 **What it does** |
| 148 | 175 |