annotate seqkit_sort.xml @ 3:29ef2c5ec205 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 771baec9a4ef7f027d05863c53fcf46ab73e561b
author iuc
date Wed, 06 Nov 2024 13:26:10 +0000
parents 1f08834f987e
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1f08834f987e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit d3d2bb547caccd2d217e5b77d62ea181f8e870c7
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1 <tool id="seqkit_sort" name="SeqKit sort" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>FASTA or FASTQ files</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="bio_tools"/>
1f08834f987e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit d3d2bb547caccd2d217e5b77d62ea181f8e870c7
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7 <expand macro="requirements"/>
1f08834f987e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit d3d2bb547caccd2d217e5b77d62ea181f8e870c7
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8 <command detect_errors="exit_code"><![CDATA[
1f08834f987e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit d3d2bb547caccd2d217e5b77d62ea181f8e870c7
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9 #set $input_fn='input.' + str($input.ext)
1f08834f987e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit d3d2bb547caccd2d217e5b77d62ea181f8e870c7
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10 #set $output_fn='seqkitsort_output.' + str($output.ext)
1f08834f987e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit d3d2bb547caccd2d217e5b77d62ea181f8e870c7
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11
1f08834f987e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit d3d2bb547caccd2d217e5b77d62ea181f8e870c7
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12 ln -s '$input' '$input_fn'
1f08834f987e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit d3d2bb547caccd2d217e5b77d62ea181f8e870c7
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13 &&
1f08834f987e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit d3d2bb547caccd2d217e5b77d62ea181f8e870c7
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14 seqkit sort
1f08834f987e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit d3d2bb547caccd2d217e5b77d62ea181f8e870c7
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15 '$input_fn'
1f08834f987e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit d3d2bb547caccd2d217e5b77d62ea181f8e870c7
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16 $reverse
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17 $sort_by
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18 -o '$output_fn'
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19 --threads \${GALAXY_SLOTS:-4}
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20
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21 ]]></command>
1f08834f987e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit d3d2bb547caccd2d217e5b77d62ea181f8e870c7
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22 <inputs>
1f08834f987e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit d3d2bb547caccd2d217e5b77d62ea181f8e870c7
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23 <param name="input" type="data" format="fasta,fasta.gz,fastqsanger,fastqsanger.gz" label="Input file"/>
1f08834f987e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit d3d2bb547caccd2d217e5b77d62ea181f8e870c7
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24 <param name="sort_by" type="select" label="Sort by:">
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25 <option value="" selected="true">Sequence ID</option>
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26 <option value="--by-bases">Non-gap bases</option>
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27 <option value="--by-length">Sequence length</option>
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28 <option value="--by-name">Full name (instead of just ID)</option>
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29 <option value="--by-seq">Sequence</option>
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30 </param>
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31 <param argument="--reverse" type="boolean" truevalue="--reverse" falsevalue="" checked="false" label="Reverse the result?"/>
1f08834f987e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit d3d2bb547caccd2d217e5b77d62ea181f8e870c7
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32 </inputs>
1f08834f987e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit d3d2bb547caccd2d217e5b77d62ea181f8e870c7
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33 <outputs>
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34 <data name="output" format_source="input" from_work_dir="seqkitsort_output.*" label="${input.name} sorted (${tool.name})"/>
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35 </outputs>
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36 <tests>
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37 <!-- 1. fastq.gz -->
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38 <test expect_num_outputs="1">
1f08834f987e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit d3d2bb547caccd2d217e5b77d62ea181f8e870c7
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39 <param name="input" value="input1.fastq.gz" ftype="fastqsanger.gz"/>
1f08834f987e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit d3d2bb547caccd2d217e5b77d62ea181f8e870c7
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40 <output name="output" file="sort_output1.fastq.gz" ftype="fastqsanger.gz"/>
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41 </test>
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42 <!-- 2. fasta.gz -->
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43 <test expect_num_outputs="1">
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44 <param name="input" value="input1.fasta.gz" ftype="fasta.gz"/>
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45 <output name="output" file="sort_output2.fasta.gz" ftype="fasta.gz"/>
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46 </test>
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47 <!-- 3. by-bases, forward, fasta -->
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48 <test expect_num_outputs="1">
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49 <param name="input" value="input1.fasta.gz" ftype="fasta.gz"/>
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50 <param name="sort_by" value="--by-bases"/>
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51 <output name="output" file="sort_output3.fasta.gz" ftype="fasta.gz"/>
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52 </test>
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53 <!-- 4. by-length, rev, fasta -->
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54 <test expect_num_outputs="1">
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55 <param name="input" value="input1.fasta.gz" ftype="fasta.gz"/>
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56 <param name="reverse" value="true"/>
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57 <param name="sort_by" value="--by-length"/>
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58 <output name="output" file="sort_output4.fasta.gz" ftype="fasta.gz"/>
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59 </test>
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60 <!-- 5. by-name, forward, fastq -->
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61 <test expect_num_outputs="1">
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62 <param name="input" value="input1.fastq.gz" ftype="fastqsanger.gz"/>
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63 <param name="sort_by" value="--by-name"/>
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64 <output name="output" file="sort_output5.fastq.gz" ftype="fastqsanger.gz"/>
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65 </test>
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66 <!-- 6. by-seq, rev, fastq -->
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67 <test expect_num_outputs="1">
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68 <param name="input" value="input1.fastq.gz" ftype="fastqsanger.gz"/>
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69 <param name="reverse" value="true"/>
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70 <param name="sort_by" value="--by-seq"/>
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71 <output name="output" file="sort_output6.fastq.gz" ftype="fastqsanger.gz"/>
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72 </test>
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73 </tests>
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74 <help>
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75 **What it does**
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76
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77 Sort sequences (FASTA, FASTQ) by id, name, sequence, or length.
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78
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79 </help>
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80 <expand macro="citations"/>
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81 </tool>