Mercurial > repos > iuc > ucsc_maffilter

annotate mafFilter.xml @ 1:fdd62fea0713 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 747e3f71fa11ce2555debdb5fdb6dce9838c71af
author iuc
date Mon, 19 Jan 2026 19:05:20 +0000
parents 9137408d4634
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9137408d4634 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
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1 <tool id="ucsc_mafFilter" name="mafFilter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.2" license="MIT">
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2 <description>Filter MAF files based on various criteria</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">482</token>
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5 <token name="@VERSION_SUFFIX@">0</token>
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6 </macros>
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7 <requirements>
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8 <requirement type="package" version="@TOOL_VERSION@">ucsc-maffilter</requirement>
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9 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[
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11 mafFilter
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12 $tolerate
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13 #if $minCol
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14 -minCol='$minCol'
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15 #end if
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16 #if $minRow
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17 -minRow='$minRow'
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18 #end if
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19 #if $maxRow
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20 -maxRow='$maxRow'
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21 #end if
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22 #if $factor_options.factor_enabled == "yes":
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23 -factor -minFactor='$minFactor'
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24 #end if
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25 #if $minScore
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26 -minScore='$minScore'
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27 #end if
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28 #if $reject
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29 -reject='$rejected_maf'
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30 #end if
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31 #if $needComp
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32 -needComp='$needComp'
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33 #end if
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34 $overlap
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35 #if $componentFilter
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36 -componentFilter='$componentFilter'
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37 #end if
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38 #if $speciesFilter
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39 -speciesFilter='$speciesFilter'
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40 #end if
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41 '$input_maf' > '$output_maf'
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42 ]]></command>
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43 <inputs>
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44 <param name="input_maf" type="data" format="maf" label="Input MAF file" help="Select the MAF file to filter."/>
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45 <param argument="-tolerate" type="boolean" truevalue="-tolerate" falsevalue="" checked="false" label="Tolerate bad input" help="Ignore bad input rather than aborting."/>
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46 <param argument="-minCol" type="integer" optional="true" value="1" min="1" label="Minimum columns" help="Filter out blocks with fewer than this number of columns."/>
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47 <param argument="-minRow" type="integer" optional="true" value="2" min="1" label="Minimum rows" help="Filter out blocks with fewer than this number of rows."/>
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48 <param argument="-maxRow" type="integer" optional="true" value="100" min="1" label="Maximum rows" help="Filter out blocks with more than or equal to this number of rows."/>
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49 <conditional name="factor_options">
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50 <param name="factor_enabled" type="select" label="Enable factor" help="Enable factor for score filtering">
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51 <option value="yes">Yes</option>
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52 <option value="no" selected="true">No</option>
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53 </param>
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54 <when value="yes">
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55 <param argument="-factor" type="boolean" truevalue="-factor" falsevalue="" label="Use factor-based score filtering" help="Filter out scores below -minFactor * (ncol^2) * nrow"/>
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56 <param argument="-minFactor" type="integer" value="5" min="0" label="Minimum factor" help="Factor to use with factor-based score filtering"/>
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57 </when>
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58 <when value="no"/>
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59 </conditional>
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60 <param argument="-minScore" type="float" label="Minimum score" help="Minimum allowed score (alternative to factor-based filtering)" optional="true"/>
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61 <param argument="-reject" type="boolean" truevalue="-reject" falsevalue="" optional="true" label="Save Rejected blocks to an output file" help="Select if you like to save rejected blocks to a file"/>
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62 <param argument="-needComp" type="text" label="Required species component" help="All alignments must have this species as one of the components" optional="true"/>
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63 <param argument="-overlap" type="boolean" truevalue="-overlap" falsevalue="" checked="false" label="Reject overlapping blocks" help="Reject overlapping blocks in reference (assumes ordered blocks)."/>
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64 <param argument="-componentFilter" type="data" format="txt" label="Component filter file" help="Filter out blocks without a component listed in this file." optional="true"/>
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65 <param argument="-speciesFilter" type="data" format="txt" label="Species filter file" help="Filter out blocks without a species listed in this file." optional="true"/>
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66 </inputs>
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67 <outputs>
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68 <data name="output_maf" format="maf" label="${tool.name} on ${on_string}: Filtered MAF output"/>
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69 <data name="rejected_maf" format="maf" label="${tool.name} on ${on_string}: Rejected blocks">
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70 <filter>reject</filter>
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71 </data>
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72 </outputs>
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73 <tests>
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74 <!-- Test 1: Testing -tolerate option on malformed MAF File -->
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75 <test expect_num_outputs="1">
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76 <param name="input_maf" value="malformed.maf"/>
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77 <param name="tolerate" value="true"/>
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78 <output name="output_maf" ftype="maf">
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79 <assert_contents>
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80 <has_n_lines n="28"/>
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81 <not_has_text text="s dog.chr6"/>
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82 </assert_contents>
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parents:
diff changeset
83 </output>
9137408d4634 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
iuc
parents:
diff changeset
84 </test>
9137408d4634 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
iuc
parents:
diff changeset
85 <!-- Test 2: Testing -minCol option on MAF File -->
9137408d4634 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
iuc
parents:
diff changeset
86 <test expect_num_outputs="1">
9137408d4634 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
iuc
parents:
diff changeset
87 <param name="input_maf" value="filter_in.maf"/>
9137408d4634 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
iuc
parents:
diff changeset
88 <param name="minCol" value="10"/>
9137408d4634 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
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diff changeset
89 <output name="output_maf" ftype="maf">
9137408d4634 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
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90 <assert_contents>
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iuc
parents:
diff changeset
91 <has_n_lines n="29"/>
9137408d4634 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
iuc
parents:
diff changeset
92 <not_has_text text="a score=500.0"/>
9137408d4634 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
iuc
parents:
diff changeset
93 <not_has_text text="s human.chr2 150 5 + 1000 ACGTA"/>
9137408d4634 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
iuc
parents:
diff changeset
94 <not_has_text text="s mouse.chr2 250 5 + 2000 ACGT-"/>
9137408d4634 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
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95 </assert_contents>
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96 </output>
9137408d4634 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
iuc
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97 </test>
9137408d4634 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
iuc
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98 <!-- Test 3: Testing -minRow option on MAF File -->
9137408d4634 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
iuc
parents:
diff changeset
99 <test expect_num_outputs="1">
9137408d4634 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
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100 <param name="input_maf" value="filter_in.maf"/>
9137408d4634 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
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101 <param name="minRow" value="3"/>
9137408d4634 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
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102 <output name="output_maf" ftype="maf">
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103 <assert_contents>
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iuc
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104 <has_n_lines n="25"/>
9137408d4634 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
iuc
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105 <not_has_text text="a score=500.0"/>
9137408d4634 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
iuc
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diff changeset
106 <not_has_text text="s human.chr2 150 5 + 1000 ACGTA"/>
9137408d4634 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
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107 <not_has_text text="s mouse.chr2 250 5 + 2000 ACGT-"/>
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iuc
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108 <not_has_text text="a score=50.0"/>
9137408d4634 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
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109 <not_has_text text="s human.chr4 110 10 + 1000 ACGTACGTAC"/>
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110 <not_has_text text="s mouse.chr4 210 10 + 2000 ACGTACGTAC"/>
9137408d4634 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
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111 </assert_contents>
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112 </output>
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113 </test>
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114 <!-- Test 4: Testing -maxRow option on MAF File -->
9137408d4634 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
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115 <test expect_num_outputs="1">
9137408d4634 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
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116 <param name="input_maf" value="filter_in.maf"/>
9137408d4634 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
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117 <param name="maxRow" value="4"/>
9137408d4634 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
iuc
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118 <output name="output_maf" ftype="maf">
9137408d4634 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
iuc
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119 <assert_contents>
9137408d4634 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
iuc
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120 <has_n_lines n="25"/>
9137408d4634 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
iuc
parents:
diff changeset
121 <has_line line="a score=50.000000"/>
9137408d4634 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
iuc
parents:
diff changeset
122 <has_line line="s human.chr4 110 10 + 1000 ACGTACGTAC"/>
9137408d4634 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
iuc
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123 <has_line line="s mouse.chr4 210 10 + 2000 ACGTACGTAC"/>
9137408d4634 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
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124 </assert_contents>
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125 </output>
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126 </test>
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iuc
parents:
diff changeset
127 <!-- Test 5: Testing -factor and -minFactor option on MAF File -->
9137408d4634 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
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128 <test expect_num_outputs="1">
9137408d4634 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
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129 <param name="input_maf" value="filter_in.maf"/>
9137408d4634 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
iuc
parents:
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130 <conditional name="factor_options">
9137408d4634 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
iuc
parents:
diff changeset
131 <param name="factor_enabled" value="yes"/>
9137408d4634 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
iuc
parents:
diff changeset
132 <param name="minFactor" value="5"/>
9137408d4634 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
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parents:
diff changeset
133 </conditional>
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iuc
parents:
diff changeset
134 <output name="output_maf" ftype="maf">
9137408d4634 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
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diff changeset
135 <assert_contents>
9137408d4634 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
iuc
parents:
diff changeset
136 <has_n_lines n="33"/>
9137408d4634 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
iuc
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diff changeset
137 </assert_contents>
9137408d4634 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
iuc
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138 </output>
9137408d4634 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
iuc
parents:
diff changeset
139 </test>
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iuc
parents:
diff changeset
140 <!-- Test 6: Testing -minScore option on MAF File -->
9137408d4634 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
iuc
parents:
diff changeset
141 <test expect_num_outputs="1">
9137408d4634 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
iuc
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diff changeset
142 <param name="input_maf" value="filter_in.maf"/>
9137408d4634 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
iuc
parents:
diff changeset
143 <param name="minScore" value="500"/>
9137408d4634 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
iuc
parents:
diff changeset
144 <output name="output_maf" ftype="maf">
9137408d4634 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
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parents:
diff changeset
145 <assert_contents>
9137408d4634 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
iuc
parents:
diff changeset
146 <has_n_lines n="23"/>
9137408d4634 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
iuc
parents:
diff changeset
147 <not_has_text text="a score=50.0"/>
9137408d4634 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
iuc
parents:
diff changeset
148 <not_has_text text="s human.chr4 110 10 + 1000 ACGTACGTAC"/>
9137408d4634 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
iuc
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diff changeset
149 <not_has_text text="s mouse.chr4 210 10 + 2000 ACGTACGTAC"/>
9137408d4634 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
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150 </assert_contents>
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parents:
diff changeset
151 </output>
9137408d4634 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
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diff changeset
152 </test>
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iuc
parents:
diff changeset
153 <!-- Test 7: Testing -reject option on MAF File -->
9137408d4634 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
iuc
parents:
diff changeset
154 <test expect_num_outputs="2">
9137408d4634 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
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parents:
diff changeset
155 <param name="input_maf" value="filter_in.maf"/>
9137408d4634 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
iuc
parents:
diff changeset
156 <param name="minScore" value="500"/>
9137408d4634 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
iuc
parents:
diff changeset
157 <param name="reject" value="true"/>
9137408d4634 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
iuc
parents:
diff changeset
158 <output name="output_maf" ftype="maf">
9137408d4634 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
iuc
parents:
diff changeset
159 <assert_contents>
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iuc
parents:
diff changeset
160 <has_n_lines n="23"/>
9137408d4634 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
iuc
parents:
diff changeset
161 <not_has_text text="a score=50.0"/>
9137408d4634 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
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parents:
diff changeset
162 <not_has_text text="s human.chr4 110 10 + 1000 ACGTACGTAC"/>
9137408d4634 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
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parents:
diff changeset
163 <not_has_text text="s mouse.chr4 210 10 + 2000 ACGTACGTAC"/>
9137408d4634 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
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parents:
diff changeset
164 </assert_contents>
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165 </output>
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parents:
diff changeset
166 <output name="rejected_maf" ftype="maf">
9137408d4634 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
iuc
parents:
diff changeset
167 <assert_contents>
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iuc
parents:
diff changeset
168 <has_n_lines n="11"/>
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169 <has_line line="a score=50.000000"/>
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170 <has_line line="s human.chr4 110 10 + 1000 ACGTACGTAC"/>
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171 <has_line line="s mouse.chr4 210 10 + 2000 ACGTACGTAC"/>
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172 </assert_contents>
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173 </output>
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174 </test>
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175 <!-- Test 8: Testing -needComp option on MAF File -->
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176 <test expect_num_outputs="1">
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177 <param name="input_maf" value="filter_in.maf"/>
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178 <param name="needComp" value="human.chr1"/>
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179 <output name="output_maf" ftype="maf">
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180 <assert_contents>
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181 <has_n_lines n="6"/>
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182 <has_text text="a score=1000.000000"/>
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183 <has_text text="s human.chr1 100 10 + 1000 ACGTACGTAC"/>
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184 <has_text text="s mouse.chr1 200 10 + 2000 ACGTACGTAC"/>
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185 <has_text text="s dog.chr1 300 10 + 3000 ACGTACGTAC"/>
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186 </assert_contents>
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187 </output>
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188 </test>
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189 <!-- Test 9: Testing -componentFilter option on MAF File -->
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190 <test expect_num_outputs="1">
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191 <param name="input_maf" value="filter_in.maf"/>
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192 <param name="componentFilter" value="componentFilter.txt"/>
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193 <output name="output_maf" ftype="maf">
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194 <assert_contents>
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195 <has_n_lines n="6"/>
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196 <has_text text="a score=1000.000000"/>
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197 <has_text text="s human.chr1 100 10 + 1000 ACGTACGTAC"/>
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198 <has_text text="s mouse.chr1 200 10 + 2000 ACGTACGTAC"/>
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199 <has_text text="s dog.chr1 300 10 + 3000 ACGTACGTAC"/>
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200 </assert_contents>
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201 </output>
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202 </test>
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203 <!-- Test 10: Testing -speciesFiler option on MAF File -->
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204 <test expect_num_outputs="1">
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205 <param name="input_maf" value="filter_in.maf"/>
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206 <param name="speciesFilter" value="speciesFilter.txt"/>
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207 <output name="output_maf" ftype="maf">
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208 <assert_contents>
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209 <has_n_lines n="25"/>
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210 <has_text text="a score=1000.000000"/>
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211 <not_has_text text="a score=500.0"/>
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212 <not_has_text text="s human.chr2 150 5 + 1000 ACGTA"/>
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213 <not_has_text text="s mouse.chr2 250 5 + 2000 ACGT-"/>
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214 <not_has_text text="a score=50.0"/>
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215 <not_has_text text="s human.chr4 110 10 + 1000 ACGTACGTAC"/>
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216 <not_has_text text="s mouse.chr4 210 10 + 2000 ACGTACGTAC"/>
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217 </assert_contents>
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218 </output>
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219 </test>
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220 </tests>
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221 <help><![CDATA[
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222 **mafFilter**
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223
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224 Filters MAF (Multiple Alignment Format) files based on specified criteria. The filtered output is written to a new MAF file, and optionally, rejected blocks are saved to a separate file.
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225
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226 **Options:**
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227
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228 - **Tolerate bad input**: Ignore bad input instead of aborting.
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229 - **Minimum columns**: Filter out blocks with fewer than the specified number of columns (default: 1).
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230 - **Minimum rows**: Filter out blocks with fewer than the specified number of rows (default: 2).
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231 - **Maximum rows**: Filter out blocks with more than or equal to the specified number of rows (default: 100).
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232 - **Factor-based score filtering**: Filter out scores below `-minFactor * (ncol^2) * nrow`.
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233 - **Minimum factor**: Factor to use with factor-based score filtering (default: 5).
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234 - **Minimum score**: Minimum allowed score (alternative to factor-based filtering).
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235 - **Rejected blocks output file**: Save rejected blocks to the specified file.
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236 - **Required species component**: All alignments must include the specified species as a component.
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237 - **Reject overlapping blocks**: Reject overlapping blocks in the reference (assumes ordered blocks).
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238 - **Component filter file**: Filter out blocks without a component listed in the provided file.
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239 - **Species filter file**: Filter out blocks without a species listed in the provided file.
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240
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241 ]]></help>
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242 <citations>
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243 <citation type="bibtex">
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244 @misc{mafFilter,
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245 author = {Kent UCSC},
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246 title = {mafFilter: A tool for filtering MAF files},
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247 note = {Tool for filtering Multiple Alignment Format files}
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248 }
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249 </citation>
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250 </citations>
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251 <creator>
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252 <person givenName="Saim" familyName="Momin" url="https://github.com/SaimMomin12"/>
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253 <organization name="Galaxy Europe" url="https://galaxyproject.org/eu/"/>
9137408d4634 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
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parents:
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254 </creator>
9137408d4634 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 62876fcda4bf5b365ef9c1bee10d611dda5453a9
iuc
parents:
diff changeset
255 </tool>