Mercurial > repos > iuc > samtools_ampliconclip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_ampliconclip commit bfe97d9abaf5d56412b48b5a011f1c4337fa5118-dirty
author iuc
date Wed, 12 Nov 2025 12:57:39 +0000
parents f20b704ba069
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1 <tool id="samtools_ampliconclip" name="Samtools ampliconclip" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>clip primer bases from bam 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="requirements"/>
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7 <expand macro="stdio"/>
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8 <expand macro="version_command"/>
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9 <command><![CDATA[
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10 @ADDTHREADS@
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11 samtools ampliconclip
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12 $hard_clip_mode
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13 #if $min_length:
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14 --fail-len $min_length
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15 #end if
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16 --tolerance $tolerance
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17 $strand
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18 -b '${input_bed}'
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19 -u
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20 $both_ends
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21 $no_excluded
5
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22 #if $write_primer_counts:
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23 --primer-counts '${primer_counts}'
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24 #end if
0
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25 -@ \$addthreads
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26 '${input_bam}'
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27 | samtools collate -@ \$addthreads -O -u -
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28 | samtools fixmate -@ \$addthreads -u - -
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29 | samtools sort -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T "\${TMPDIR:-.}" -o '${output_bam}'
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30 ]]></command>
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31 <inputs>
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32 <param name="input_bed" type="data" format="bed" label="Genetic intervals (in BED format)" />
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33 <param name="input_bam" type="data" format="bam" label="BAM file" />
5
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34 <param name="hard_clip_mode" argument="--hard-clip" type="boolean" checked="false" truevalue="--hard-clip" falsevalue="--soft-clip" label="hard clip" help="hard clip (remove bases), unchecked = default soft-clipping" />
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35 <param argument="--strand" type="boolean" checked="false" truevalue="--strand" falsevalue="" label="only clip reads that match bed file strand annotation" />
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36 <param argument="--both-ends" type="boolean" checked="false" truevalue="--both-ends" falsevalue="" label="clip both ends of reads (false = 5' only)" />
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37 <param argument="--no-excluded" type="boolean" checked="false" truevalue="--no-excluded" falsevalue="" label="don't write excluded reads to output (default = write all)" />
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38 <param name="min_length" argument="--fail-len" type="integer" min="0" optional="true" label="Min Read length" help="mark reads QCFAIL at this length or shorter after clipping" />
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39 <param argument="--tolerance" type="integer" value="5" min="0" label="Tolerance" help="match region within this number of bases, default 5." />
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40 <param name="write_primer_counts" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Write primer counts" help="If enabled, write primer counts to output file." />
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41 </inputs>
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42 <outputs>
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43 <data name="output_bam" format="bam" />
5
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44 <data name="primer_counts" format="bedgraph" label="${tool.name} on ${on_string}: Primer counts">
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45 <filter>write_primer_counts</filter>
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46 </data>
0
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47 </outputs>
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48 <tests>
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49 <!-- 1) -->
5
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50 <test expect_num_outputs="1">
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51 <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
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52 <param name="input_bam" value="eboVir3.bam" ftype="bam" />
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53 <output name="output_bam" file="eboVir3.clipped.bam" ftype="bam" lines_diff="22" />
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54 </test>
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55 <!-- 2) testing strand -->
5
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56 <test expect_num_outputs="1">
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57 <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
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58 <param name="input_bam" value="eboVir3.bam" ftype="bam" />
4
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59 <param name="strand" value="true" />
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60 <output name="output_bam" file="eboVir3.clipped.strand.bam" ftype="bam" lines_diff="16" />
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61 </test>
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62 <!-- 3) testing hard clip-->
5
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63 <test expect_num_outputs="1">
0
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64 <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
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65 <param name="input_bam" value="eboVir3.bam" ftype="bam" />
4
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66 <param name="hard_clip_mode" value="true" />
0
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67 <output name="output_bam" file="eboVir3.hardclipped.bam" ftype="bam" lines_diff="14" />
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68 </test>
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69 <!-- 4) testing strand and min length-->
5
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70 <test expect_num_outputs="1">
0
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71 <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
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72 <param name="input_bam" value="eboVir3.bam" ftype="bam" />
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73 <param name="min_length" value="30" />
4
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74 <param name="strand" value="true" />
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75 <param name="tolerance" value="6" />
4
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76 <param name="both_ends" value="true" />
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77 <param name="no_excluded" value="true" />
0
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78 <output name="output_bam" file="eboVir3.clipped.strand_gt30.bam" ftype="bam" lines_diff="13" />
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79 </test>
5
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80 <!-- 5) testing write_primer_counts -->
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81 <test expect_num_outputs="2">
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82 <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
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83 <param name="input_bam" value="eboVir3.bam" ftype="bam" />
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84 <param name="write_primer_counts" value="true" />
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85 <output name="output_bam" file="eboVir3.clipped.bam" ftype="bam" lines_diff="22" />
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86 <output name="primer_counts" file="eboVir3.primer_counts.txt" ftype="bedgraph" />
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87 </test>
0
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88 </tests>
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89 <help>
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90 **What it does**
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91 Clips read alignments where they match BED file defined regions (e.g. for amplicon sequencing).
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92
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93 samtools ampliconclip -b [INPUT BED] [INPUT BAM1] -o [OUTPUT]
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94 </help>
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95 <expand macro="citations"/>
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96 </tool>