Mercurial > repos > jjohnson > mothur_toolsuite
annotate mothur/tools/mothur/screen.seqs.xml @ 0:3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
author | jjohnson |
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date | Tue, 07 Jun 2011 17:32:23 -0400 |
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children | fcc0778f6987 |
rev | line source |
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0
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1 <tool id="mothur_screen_seqs" name="Screen.seqs" version="1.15.0"> |
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2 <description>Screen sequences</description> |
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3 <command interpreter="python"> |
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4 mothur_wrapper.py |
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5 #import re, os.path |
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6 --cmd='screen.seqs' |
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7 #set results = ["'^mothur.\S+\.logfile$:'" + $logfile.__str__] |
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8 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.good.\2',$os.path.basename($input.__str__)) + ":'" + $out_file.__str__] |
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9 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.bad.accnos',$os.path.basename($input.__str__)) + ":'" + $bad_accnos.__str__] |
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10 --outputdir='$logfile.extra_files_path' |
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11 --tmpdir='${logfile.extra_files_path}/input' |
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12 --fasta=$input |
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13 #if int($start) >= 0: |
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14 --start=$start |
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15 #end if |
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16 #if int($end) >= 0: |
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17 --end=$end |
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18 #end if |
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19 #if int($minlength) >= 0: |
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20 --minlength=$minlength |
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21 #end if |
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22 #if int($maxlength) >= 0: |
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23 --maxlength=$maxlength |
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24 #end if |
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25 #if int($maxambig) >= 0: |
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26 --maxambig=$maxambig |
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27 #end if |
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28 #if int($maxhomop) >= 0: |
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29 --maxhomop=$maxhomop |
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30 #end if |
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31 #if int($criteria) >= 0: |
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32 --criteria=$criteria |
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33 #end if |
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34 #if $optimize != None and $optimize.__str__ != "None": |
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35 --optimize=$optimize |
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36 #end if |
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37 #if $input_names != None and $input_names.__str__ != "None": |
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38 --name=$input_names |
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39 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.good.\2',$os.path.basename($input_names.__str__)) + ":'" + $output_names.__str__] |
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40 #end if |
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41 #if $input_groups != None and $input_groups.__str__ != "None": |
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42 --group=$input_groups |
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43 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.good.\2',$os.path.basename($input_groups.__str__)) + ":'" + $output_groups.__str__] |
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44 #end if |
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45 #if $input_alignreport != None and $input_alignreport.__str__ != "None": |
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46 --alignreport=$input_alignreport |
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47 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.good.\2',$os.path.basename($input_alignreport.__str__)) + ":'" + $output_alignreport.__str__] |
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48 #end if |
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49 --result=#echo ','.join($results) |
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50 </command> |
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51 <inputs> |
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52 <param name="input" type="data" format="fasta,align" label="fasta - Fasta to screen"/> |
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53 <param name="start" type="integer" value="-1" label="start - Remove sequences that start after position (ignored when negative)"/> |
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54 <param name="end" type="integer" value="-1" label="end - Remove sequences that end before position (ignored when negative)"/> |
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55 <param name="minlength" type="integer" value="-1" label="minlength - Remove sequences shorter than (ignored when negative)"/> |
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56 <param name="maxlength" type="integer" value="-1" label="maxlength - Remove sequences longer than (ignored when negative)"/> |
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57 <param name="maxambig" type="integer" value="-1" label="maxambig - Remove sequences with ambiguous bases greater than (ignored when negative)"/> |
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58 <param name="maxhomop" type="integer" value="-1" label="maxhomop - Remove sequences with homopolymers greater than (ignored when negative)"/> |
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59 <param name="criteria" type="integer" value="-1" label="criteria - Percent of sequences that an optimize value must match to be retained(ignored when negative)"/> |
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60 <param name="optimize" type="select" multiple="true" display="checkboxes" label="optimize - Optimize selected paramenters"> |
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61 <option value="start">start</option> |
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62 <option value="end">end</option> |
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63 <option value="minlength">minlength</option> |
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64 <option value="maxlength">maxlength</option> |
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65 <option value="maxambig">maxambig</option> |
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66 <option value="maxhomop">maxhomop</option> |
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67 </param> |
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68 <param name="input_names" type="data" format="names" optional="true" label="name - Sequece Names to screen"/> |
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69 <param name="input_groups" type="data" format="groups" optional="true" label="group - Groups to screen"/> |
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70 <param name="input_alignreport" type="data" format="align.report" optional="true" label="alignreport - Align Report to screen"/> |
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71 </inputs> |
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72 <outputs> |
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73 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
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74 <data format="fasta" name="out_file" label="${tool.name} on ${on_string}: good.fasta" > |
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75 <change_format> |
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76 <when input_dataset="input" attribute="ext" value="align" format="align"/> |
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77 </change_format> |
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78 <!-- |
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79 <actions> |
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80 <conditional name="input"> |
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81 <when datatype_isinstance="align"> |
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82 <action type="format" default="align"/> |
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83 </when> |
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84 </conditional> |
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85 </actions> |
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86 --> |
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87 </data> |
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88 <data format="accnos" name="bad_accnos" label="${tool.name} on ${on_string}: bad.accnos" /> |
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89 <data format="names" name="output_names" label="${tool.name} on ${on_string}: names" > |
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90 <filter>input_names != None</filter> |
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91 </data> |
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92 <data format="groups" name="output_groups" label="${tool.name} on ${on_string}: groups" > |
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93 <filter>input_groups != None</filter> |
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94 </data> |
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95 <data format="align.report" name="output_alignreport" label="${tool.name} on ${on_string}: align.report" > |
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96 <filter>input_alignreport != None</filter> |
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97 </data> |
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98 </outputs> |
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99 <requirements> |
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100 <requirement type="binary">mothur</requirement> |
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101 </requirements> |
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102 <tests> |
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103 </tests> |
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104 <help> |
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105 **Mothur Overview** |
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106 |
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107 Mothur_, initiated by Dr. Patrick Schloss and his software development team |
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108 in the Department of Microbiology and Immunology at The University of Michigan, |
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109 provides bioinformatics for the microbial ecology community. |
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110 |
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111 .. _Mothur: http://www.mothur.org/wiki/Main_Page |
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112 |
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113 **Command Documenation** |
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114 |
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115 The screen.seqs_ command enables you to keep sequences that fulfill certain user defined criteria. Furthermore, it enables you to cull those sequences not meeting the criteria from a names, group, or align.report file. |
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116 |
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117 .. _screen.seqs: http://www.mothur.org/wiki/Screen.seqs |
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118 |
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119 |
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120 </help> |
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121 </tool> |