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annotate tools/mothur/screen.seqs.xml @ 0:ee4fee239fe7 draft default tip

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planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
author sanbi-uwc
date Fri, 03 Jun 2016 09:32:47 -0400
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1 <tool profile="16.07" id="mothur_screen_seqs" name="Screen.seqs" version="@WRAPPER_VERSION@.0">
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2 <description>Screen sequences</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="version_command"/>
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8 <command detect_errors="aggressive"><![CDATA[
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9 echo 'screen.seqs(
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10 fasta=$fasta_in
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11 #if $start > -1:
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12 ,start=$start
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13 #end if
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14 #if $end > -1:
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15 ,end=$end
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16 #end if
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17 #if $minlength > -1:
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18 ,minlength=$minlength
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19 #end if
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20 #if $maxlength > -1:
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21 ,maxlength=$maxlength
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22 #end if
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23 #if $maxambig > -1:
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24 ,maxambig=$maxambig
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25 #end if
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26 #if $maxhomop > -1:
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27 ,maxhomop=$maxhomop
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28 #end if
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29 #if $criteria > -1:
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30 ,criteria=$criteria
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31 #end if
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32 #if $optimize:
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33 ,optimize=$optimize
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34 #end if
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35 #if $qfile_in:
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36 ,qfile=$qfile_in
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37 #end if
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38 #if $names_in:
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39 ,name=$names_in
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40 #end if
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41 #if $groups_in:
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42 ,group=$groups_in
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43 #end if
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44 #if $alignreport_in:
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45 ,alignreport=$alignreport_in
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46 #end if
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47 #if $taxonomy_in:
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48 ,taxonomy=$taxonomy_in
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49 #end if
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50 #if $count_in:
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51 ,count=$count_in
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52 #end if
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53 #if $summary:
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54 ,summary=$summary
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55 #end if
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56 #if $contigsreport:
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57 ,contigsreport=$contigsreport
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58 #end if
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59 ,processors='"\${GALAXY_SLOTS:-8}"'
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60 )'
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61 | sed 's/ //g' ## mothur trips over whitespace
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62 | mothur &&
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63
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64 ## move output files to correct destination
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65 mv mothur.*.logfile "$logfile" &&
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66 prefix="$fasta_in" &&
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67 mv \${prefix%.dat}*.good.* "$fasta_out" &&
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68 mv \${prefix%.dat}*.bad.accnos "$bad_accnos"
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69 #if $qfile_in:
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70 && prefix="$qfile_in" && mv \${prefix%.dat}*.good.* "$qfile_out"
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71 #end if
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72 #if $names_in:
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73 && prefix="$names_in" && mv \${prefix%.dat}*.good.* "$names_out"
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74 #end if
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75 #if $groups_in:
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76 && prefix="$groups_in" && mv \${prefix%.dat}*.good.* "$groups_out"
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77 #end if
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78 #if $alignreport_in:
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79 && prefix="$alignreport_in" && mv \${prefix%.dat}*.good.* "$alignreport_out"
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80 #end if
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81 #if $taxonomy_in:
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82 && prefix="$taxonomy_in" && mv \${prefix%.dat}*.good.* "$taxonomy_out"
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83 #end if
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84 #if $count_in:
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85 && prefix="$count_in" && mv \${prefix%.dat}*.good.* "$count_out"
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86 #end if
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87 ]]></command>
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88 <inputs>
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89 <param name="fasta_in" type="data" format="fasta,mothur.align" label="fasta - Fasta to screen"/>
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90 <param name="start" type="integer" value="-1" label="start - Remove sequences that start after position (ignored when negative)"/>
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91 <param name="end" type="integer" value="-1" label="end - Remove sequences that end before position (ignored when negative)"/>
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92 <param name="minlength" type="integer" value="-1" label="minlength - Remove sequences shorter than (ignored when negative)"/>
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93 <param name="maxlength" type="integer" value="-1" label="maxlength - Remove sequences longer than (ignored when negative)"/>
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94 <param name="maxambig" type="integer" value="-1" label="maxambig - Remove sequences with ambiguous bases greater than (ignored when negative)"/>
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95 <param name="maxhomop" type="integer" value="-1" label="maxhomop - Remove sequences with homopolymers greater than (ignored when negative)"/>
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96 <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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97 <param name="optimize" type="select" multiple="true" display="checkboxes" label="optimize - Optimize selected paramenters">
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98 <option value="start">start</option>
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99 <option value="end">end</option>
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100 <option value="minlength">minlength</option>
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101 <option value="maxlength">maxlength</option>
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102 <option value="maxambig">maxambig</option>
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103 <option value="maxhomop">maxhomop</option>
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104 </param>
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105 <param name="qfile_in" type="data" format="qual" optional="true" label="qfile - Sequence Quality file to screen"/>
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106 <param name="names_in" type="data" format="mothur.names" optional="true" label="name - Sequence Names to screen"/>
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107 <param name="groups_in" type="data" format="mothur.groups" optional="true" label="group - Groups to screen"/>
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108 <param name="alignreport_in" type="data" format="mothur.align.report" optional="true" label="alignreport - Align Report to screen"/>
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109 <param name="summary" type="data" format="mothur.summary" optional="true" label="summary - allows you to enter the summary file created by summary.seqs to save processing time when screening with parameters in the summary file"/>
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110 <param name="contigsreport" type="data" format="contigs.report" optional="true" label="contigsreport - file is created by the make.contigs command. If you provide the contigs report file you can screen your sequences using the following parameters: minoverlap, ostart, oend and mismatches"/>
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111 <param name="taxonomy_in" type="data" format="taxonomy" optional="true" label="taxonomy - Taxonomy to screen"/>
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112 <param name="count_in" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
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113 </inputs>
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114 <outputs>
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115 <data name="logfile" format="txt" label="${tool.name} on ${on_string}: logfile"/>
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116 <data name="fasta_out" format_source="fasta_in" label="${tool.name} on ${on_string}: good.${fasta_in.datatype.file_ext}"/>
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117 <data name="bad_accnos" format="mothur.accnos" label="${tool.name} on ${on_string}: bad.accnos"/>
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118 <data name="qfile_out" format_source="qfile_in" label="${tool.name} on ${on_string}: qfile">
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119 <filter>qfile_in</filter>
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120 </data>
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121 <data name="names_out" format="mothur.names" label="${tool.name} on ${on_string}: names">
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122 <filter>names_in</filter>
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123 </data>
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124 <data name="groups_out" format="mothur.groups" label="${tool.name} on ${on_string}: groups">
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125 <filter>groups_in</filter>
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126 </data>
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127 <data name="alignreport_out" format="mothur.align.report" label="${tool.name} on ${on_string}: align.report">
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128 <filter>alignreport_in</filter>
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129 </data>
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130 <data name="count_out" format="count" label="${tool.name} on ${on_string}: count">
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131 <filter>count_in</filter>
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132 </data>
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133 </outputs>
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134 <tests>
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135 <test>
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136 <param name="fasta_in" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta"/>
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137 <param name="maxambig" value="0"/>
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138 <param name="maxlength" value="275"/>
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139 <output name="fasta_out" file="Mock_S280_L001_R1_001_small.trim.contigs.good.fasta"/>
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140 <output name="bad_accnos" file="Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos"/>
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141 <expand macro="logfile-test"/>
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142 </test>
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143 <test>
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144 <param name="fasta_in" value="amazon.fasta"/>
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145 <param name="count_in" value="amazon.count_table"/>
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146 <param name="maxambig" value="0"/>
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147 <param name="maxlength" value="275"/>
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148 <output name="fasta_out" md5="d41d8cd98f00b204e9800998ecf8427e"/>
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149 <output name="count_out" md5="5f4a08bbf3ec12f954edbcc6b2a2feee"/>
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150 <output name="bad_accnos" md5="66acde5349e34fc97be22032ce68eea5"/>
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151 <expand macro="logfile-test"/>
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152 </test>
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153 </tests>
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154 <help>
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155 <![CDATA[
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156
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157 @MOTHUR_OVERVIEW@
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158
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159 **Command Documenation**
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160
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161 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 name_, group_, or align.report_ file.
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162
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163 .. _name: http://www.mothur.org/wiki/Name_file
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164 .. _group: http://www.mothur.org/wiki/Group_file
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165 .. _align.report: http://www.mothur.org/wiki/Align.seqs
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166 .. _screen.seqs: http://www.mothur.org/wiki/Screen.seqs
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167
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168 ]]>
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169 </help>
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170 <expand macro="citations"/>
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171 </tool>