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annotate maf-convert.xml @ 4:8705e0d74a0f draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 6b601baaf89634bc8d110ea06e3e64c7a585f3ba"
author iuc
date Wed, 24 Mar 2021 22:36:50 +0000
parents 9a7e91fc6562
children f5a5a2b39ff2
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8705e0d74a0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 6b601baaf89634bc8d110ea06e3e64c7a585f3ba"
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1 <tool id="last_maf_convert" name="MAF-convert" version="@LAST_CONDA_VERSION@+galaxy0" profile="20.01">
0
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3 <description>read MAF-format alignments and write them in another format.</description>
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5 <macros>
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6 <import>macros_last.xml</import>
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7 </macros>
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8
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9 <requirements>
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10 <requirement type="package" version="@LAST_CONDA_VERSION@">last</requirement>
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11 </requirements>
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12
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13 <command detect_errors="exit_code"><![CDATA[
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14 maf-convert
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16 $maf_convert.output_type.output_format
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18 $maf_convert.noheader
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20 #if $maf_convert.output_type.output_format == 'psl'
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21 $maf_convert.output_type.protein
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22 -j $maf_convert.output_type.j
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23 #end if
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25 #if $maf_convert.output_type.output_format == 'sam'
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26 $maf_convert.output_type.sam_file.dictionary
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27 #if $maf_convert.output_type.sam_file.dictionary == '-d'
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28 -f $maf_convert.output_type.sam_file.f
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29 #end if
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30 #if $maf_convert.output_type.readfile != ''
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31 -r $maf_convert.output_type.r
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32 #end if
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33 #end if
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35 #if $maf_convert.output_type.output_format == 'blast' or $maf_convert.output_type.output_format == 'html'
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36 -l $maf_convert.output_type.l
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37 #end if
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38
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39 '$maf_file'
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9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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41 > '$outfile'
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42
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43 ]]></command>
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44 <inputs>
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45 <param name="maf_file" type="data" format="maf" label="MAF file to convert" />
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46
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47 <section name="maf_convert" title="MAF-convert arguments" expanded="true">
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48
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49 <param name="noheader" argument="-n" type="boolean" truevalue="-n" falsevalue="" checked="false" label="No header." help="Omit any header lines from the output"/>
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50
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51 <conditional name="output_type">
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52 <param name="output_format" type="select" multiple="false" label="Output format">
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53 <option value="axt">axt</option>
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54 <option value="blast">blast</option>
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55 <option value="blasttab">blasttab</option>
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56 <option value="chain">chain</option>
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57 <option value="html">html</option>
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58 <option value="psl" selected="true">psl</option>
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59 <option value="sam">sam</option>
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60 <option value="tab">tab</option>
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61 </param>
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62 <when value="blast">
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63 <param argument="-l" type="integer" value="60" label="Line length"/>
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64 </when>
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65 <when value="html">
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66 <param argument="-l" type="integer" value="60" label="Line length"/>
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67 </when>
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68 <when value="psl">
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69 <param name="protein" argument="-p" type="boolean" truevalue="-p" falsevalue="" checked="false" label="Protein alignments." />
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70 <param argument="-j" type="integer" value="1" label="Join neighboring alignments" help="Join neighboring alignments if they are co-linear and separated by at most N letters."/>
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71 </when>
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72 <when value="sam">
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73 <conditional name="sam_file">
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74 <param name="dictionary" argument="-d" type="boolean" truevalue="-d" falsevalue="" checked="false" label="Include dictionary of sequence lengths in sam format"/>
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75 <when value="-d">
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76 <param argument="-f" type="data" format="dict" label="Get a sequence dictionary from DICTFILE" />
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77 </when>
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78 </conditional>
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79 <param argument="-r" type="text" value="" label="Specify read group information" help="Example: 'ID:1 PL:ILLUMINA SM:mysample'"/>
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80 </when>
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81 </conditional>
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82 </section>
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83 </inputs>
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84
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85 <outputs>
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86 <data format="maf" name="outfile" label="${on_string} to ${maf_convert.output_type.output_format}">
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87 <change_format>
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88 <when input="maf_convert.output_type.output_format" value="axt" format="axt" />
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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89 <when input="maf_convert.output_type.output_format" value="blast" format="blastxml" />
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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90 <when input="maf_convert.output_type.output_format" value="blasttab" format="blastxml" />
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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91 <when input="maf_convert.output_type.output_format" value="chain" format="txt" />
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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92 <when input="maf_convert.output_type.output_format" value="html" format="html" />
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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93 <when input="maf_convert.output_type.output_format" value="psl" format="tabular" />
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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94 <when input="maf_convert.output_type.output_format" value="sam" format="sam" />
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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95 <when input="maf_convert.output_type.output_format" value="tab" format="tabular" />
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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96 </change_format>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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97 </data>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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98 </outputs>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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99
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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100 <tests>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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101 <test>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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102 <param name="maf_file" value="last_align_train_gen.maf" ftype="maf"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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103 <section name="maf_convert">
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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104 <conditional name="output_type">
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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105 <param name="output_format" value="axt"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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106 </conditional>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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107 </section>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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108 <output name="outfile" file="outfile_convert.axt"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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109 </test>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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110 <test>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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111 <param name="maf_file" value="last_align_train_gen.maf" ftype="maf"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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112 <section name="maf_convert">
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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113 <conditional name="output_type">
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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114 <param name="output_format" value="blast"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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115 </conditional>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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116 </section>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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117 <output name="outfile" file="outfile_convert.blast"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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118 </test>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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119 <test>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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120 <param name="maf_file" value="last_align_train_gen.maf" ftype="maf"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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121 <section name="maf_convert">
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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122 <conditional name="output_type">
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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123 <param name="output_format" value="html"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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124 </conditional>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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125 </section>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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126 <output name="outfile" file="outfile_convert.html"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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127 </test>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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128 <test>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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129 <param name="maf_file" value="last_align_train_gen.maf" ftype="maf"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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130 <section name="maf_convert">
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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131 <conditional name="output_type">
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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132 <param name="output_format" value="tab"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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133 </conditional>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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134 </section>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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135 <output name="outfile" file="outfile_convert.tab"/>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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136 </test>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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137 </tests>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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138
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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139 <help><![CDATA[
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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140 This script reads alignments in maf format, and writes them in another format. It can write them in these formats: axt, blast, blasttab, chain, html, psl, sam, tab.
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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141 ]]></help>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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142 <citations><expand macro="citations"/></citations>
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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143 </tool>